bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of
trmE
for Growth of the Psychrophile
Pseudomonas syringae
at Low Temperatures
Authors: Singh Ashish K. , Pindi Pavan Kumar , Dube Smita , Sundareswaran V. R. , Shivaji S. 
Published: May 2009

ABSTRACT

Transposon mutagenesis of
Pseudomonas syringae
Lz4W, a psychrophilic bacterium capable of growing at temperatures between 2 and 30°C, yielded 30 cold-sensitive mutants, and CSM1, one of these cold-sensitive mutants, was characterized. Growth of CSM1 was retarded when it was cultured at 4°C but not when it was cultured at 22°C and 28°C compared to the growth of wild-type cells, indicating that CSM1 is a cold-sensitive mutant of
P. syringae
Lz4W. The mutated gene in CSM1 was identified as
trmE
(coding for tRNA modification GTPase), and evidence is provided that this gene is induced at low temperatures. Further, the cold-inducible nature of the
trmE
promoter was demonstrated. In addition, the transcription start site and the various regulatory elements of the
trmE
promoter, such as the −10 region, −35 region, UP element, cold box, and DEAD box, were identified, and the importance of these regulatory elements in promoter activity were confirmed. The importance of
trmE
in rapid adaptation to growth at low temperatures was further highlighted by plasmid-mediated complementation that alleviated the cold-sensitive phenotype of CSM1.
Aerobic Mineralization of Hexachlorobenzene by Newly Isolated Pentachloronitrobenzene-Degrading
Nocardioides
sp. Strain PD653
Authors: Takagi Kazuhiro , Iwasaki Akio , Kamei Ichiro , Satsuma Koji , Yoshioka Yuichi , Harada Naoki 
Published: May 2009

ABSTRACT

A novel aerobic pentachloronitrobenzene-degrading bacterium,
Nocardioides
sp. strain PD653, was isolated from an enrichment culture in a soil-charcoal perfusion system. The bacterium also degraded hexachlorobenzene, a highly recalcitrant environmental pollutant, accompanying the generation of chloride ions. Liberation of
14
CO
2
from [U-ring-
14
C]hexachlorobenzene was detected in a culture of the bacterium and indicates that strain PD653 is able to mineralize hexachlorobenzene under aerobic conditions. The metabolic pathway of hexachlorobenzene is initiated by oxidative dechlorination to produce pentachlorophenol. As further intermediate metabolites, tetrachlorohydroquinone and 2,6-dichlorohydroquinone have been detected. Strain PD653 is the first naturally occurring aerobic bacteria capable of mineralizing hexachlorobenzene.
Staphylococcus aureus
Virulence Expression Is Impaired by
Lactococcus lactis
in Mixed Cultures
Authors: Even Sergine , Charlier Cathy , Nouaille Sébastien , Ben Zakour Nouri L. , Cretenet Marina , Cousin Fabien J. , Gautier Michel , Cocaign-Bousquet Muriel , Loubière Pascal , Le Loir Yves 
Published: May 2009

ABSTRACT

Staphylococcus aureus
is responsible for numerous food poisonings due to the production of enterotoxins by strains contaminating foodstuffs, especially dairy products. Several parameters, including interaction with antagonistic flora such as
Lactococcus lactis
, a lactic acid bacterium widely used in the dairy industry, can modulate
S. aureus
proliferation and virulence expression. We developed a dedicated
S. aureus
microarray to investigate the effect of
L. lactis
on staphylococcal gene expression in mixed cultures. This microarray was used to establish the transcriptomic profile of
S. aureus
in mixed cultures with
L. lactis
in a chemically defined medium held at a constant pH (6.6). Under these conditions,
L. lactis
hardly affected
S. aureus
growth. The expression of most genes involved in the cellular machinery, carbohydrate and nitrogen metabolism, and stress responses was only slightly modulated: a short time lag in mixed compared to pure cultures was observed. Interestingly, the induction of several virulence factors and regulators, including the
agr
locus,
sarA
, and some enterotoxins, was strongly affected. This work clearly underlines the complexity of
L. lactis
antagonistic potential for
S. aureus
and yields promising leads for investigations into nonantibiotic biocontrol of this major pathogen.
Fermentation pH Influences the Physiological-State Dynamics of
Lactobacillus bulgaricus
CFL1 during pH-Controlled Culture
Authors: Rault Aline , Bouix Marielle , Béal Catherine 
Published: May 2009

ABSTRACT

This study aims at better understanding the effects of fermentation pH and harvesting time on
Lactobacillus bulgaricus
CFL1 cellular state in order to improve knowledge of the dynamics of the physiological state and to better manage starter production. The Cinac system and multiparametric flow cytometry were used to characterize and compare the progress of the physiological events that occurred during pH 6 and pH 5 controlled cultures. Acidification activity, membrane damage, enzymatic activity, cellular depolarization, intracellular pH, and pH gradient were determined and compared during growing conditions. Strong differences in the time course of viability, membrane integrity, and acidification activity were displayed between pH 6 and pH 5 cultures. As a main result, the pH 5 control during fermentation allowed the cells to maintain a more robust physiological state, with high viability and stable acidification activity throughout growth, in opposition to a viability decrease and fluctuation of activity at pH 6. This result was mainly explained by differences in lactate concentration in the culture medium and in pH gradient value. The elevated content of the ionic lactate form at high pH values damaged membrane integrity that led to a viability decrease. In contrast, the high pH gradient observed throughout pH 5 cultures was associated with an increased energetic level that helped the cells maintain their physiological state. Such results may benefit industrial starter producers and fermented-product manufacturers by allowing them to better control the quality of their starters, before freezing or before using them for food fermentation.
CO2Uptake and Fixation by a Thermoacidophilic Microbial Community Attached to Precipitated Sulfur in a Geothermal Spring
Authors: Boyd Eric S. , Leavitt William D. , Geesey Gill G. 
Published: May 2009

ABSTRACTCarbon fixation at temperatures above 73°C, the upper limit for photosynthesis, is carried out by chemosynthetic thermophiles. Yellowstone National Park (YNP), Wyoming possesses many thermal features that, while too hot for photosynthesis, presumably support chemosynthetic-based carbon fixation. To our knowledge, in situ rates of chemosynthetic reactions at these high temperatures in YNP or other high-temperature terrestrial geothermal springs have not yet been reported. A microbial community attached to precipitated elemental sulfur (Sofloc) at the source of Dragon Spring (73°C, pH 3.1) in Norris Geyser Basin, YNP, exhibited a maximum rate of CO2uptake of 21.3 ± 11.9 μg of C 107cells−1h−1. When extrapolated over the estimated total quantity of Sofloc at the spring's source, the Sofloc-associated microbial community accounted for the uptake of 121 mg of C h−1at this site. On a per-cell basis, the rate was higher than that calculated for a photosynthetic mat microbial community dominated bySynechococcusspp. in alkaline springs at comparable temperatures. A portion of the carbon taken up as CO2by the Sofloc-associated biomass was recovered in the cellular nucleic acid pool, demonstrating that uptake was coupled to fixation. The most abundant sequences in a 16S rRNA clone library of the Sofloc-associated community were related to chemolithoautotrophicHydrogenobaculumstrains previously isolated from springs in the Norris Geyser Basin. These microorganisms likely contributed to the uptake and fixation of CO2in this geothermal habitat.
Bar-Coded Pyrosequencing Reveals Shared Bacterial Community Properties along the Temperature Gradients of Two Alkaline Hot Springs in Yellowstone National Park
Authors: Miller Scott R. , Strong Aaron L. , Jones Kenneth L. , Ungerer Mark C. 
Published: May 2009

ABSTRACT

An understanding of how communities are organized is a fundamental goal of ecology but one which has historically been elusive for microbial systems. We used a bar-coded pyrosequencing approach targeting the V3 region of the bacterial small-subunit rRNA gene to address the factors that structure communities along the thermal gradients of two alkaline hot springs in the Lower Geyser Basin of Yellowstone National Park. The filtered data set included a total of nearly 34,000 sequences from 39 environmental samples. Each was assigned to one of 391 operational taxonomic units (OTUs) identified by their unique V3 sequence signatures. Although the two hot springs differed in their OTU compositions, community resemblance and diversity changed with strikingly similar dynamics along the two outflow channels. Two lines of evidence suggest that these community properties are controlled primarily by environmental temperature. First, community resemblance decayed exponentially with increasing differences in temperature between samples but was only weakly correlated with physical distance. Second, diversity decreased with increasing temperature at the same rate along both gradients but was uncorrelated with other measured environmental variables. This study also provides novel insights into the nature of the ecological interactions among important taxa in these communities. A strong negative association was observed between cyanobacteria and the
Chloroflexi
, which together accounted for ∼70% of the sequences sampled. This pattern contradicts the longstanding hypothesis that coadapted lineages of these bacteria maintain tightly cooccurring distributions along these gradients as a result of a producer-consumer relationship. We propose that they instead compete for some limiting resource(s).
Direct Effects of UV-B Radiation on the Freshwater Heterotrophic NanoflagellateParaphysomonassp
Authors: Macaluso Amy L. , Mitchell David L. , Sanders Robert W. 
Published: May 2009

ABSTRACTThe formation of DNA photoproducts in organisms exposed to ambient levels of UV-B radiation can lead to death and/or reduced population growth in aquatic systems. Dependence on photoenzymatic repair to reverse DNA damage caused by UV-B radiation is demonstrated forParaphysomonassp., a member of a widely distributed genus of heterotrophic nanoflagellates. At 20°C,Paraphysomonassp. was exposed to a range of UV-B intensities encountered in natural systems. Populations of the flagellate survived and grew in a dose-dependent manner, but only when simultaneously exposed to photorepair radiation (PRR). In contrast, flagellates exposed to UV-B at 15°C suffered 100% mortality except at the lowest UV-B level (with PRR) tested, which suggested a photorepair temperature optimum above 15°C. After acute UV-B exposures, DNA damage (measured as the formation of pyrimidine dimers) was reduced only in organisms that underwent subsequent exposure to PRR. Populations kept in the dark after UV-B exposure maintained the initial levels of pyrimidine dimers. These results are the first to demonstrate the reliance of a heterotrophic flagellate on photoenzymatic DNA repair for survival from UV-B exposure.
Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “
Leptospirillum rubarum
” (Group II) and “
Leptospirillum ferrodiazotrophum
” (Group III) Bacteria in Acid Mine Drainage Biofilms
Authors: Goltsman Daniela S. Aliaga , Denef Vincent J. , Singer Steven W. , VerBerkmoes Nathan C. , Lefsrud Mark , Mueller Ryan S. , Dick Gregory J. , Sun Christine L. , Wheeler Korin E. , Zemla Adam , Baker Brett J. , Hauser Loren , Land Miriam , Shah Manesh B. , Thelen Michael P. , Hettich Robert L. , Banfield Jillian F. 
Published: May 2009

ABSTRACT

We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing
Leptospirillum
group II and III bacteria (phylum
Nitrospirae
) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of
Leptospirillum
groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both
Leptospirillum
types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in
Leptospirillum
group III, consistent with its distribution in gradients within biofilms. Interestingly,
Leptospirillum
group II uses a methyl-dependent and
Leptospirillum
group III a methyl-independent response pathway. Although only
Leptospirillum
group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of
Leptospirillum
groups II and III.
Analysis of Flagellar Phosphoproteins from
Chlamydomonas reinhardtii
Authors: Boesger Jens , Wagner Volker , Weisheit Wolfram , Mittag Maria 
Published: May 2009

ABSTRACT

Cilia and flagella are cell organelles that are highly conserved throughout evolution. For many years, the green biflagellate alga
Chlamydomonas reinhardtii
has served as a model for examination of the structure and function of its flagella, which are similar to certain mammalian cilia. Proteome analysis revealed the presence of several kinases and protein phosphatases in these organelles. Reversible protein phosphorylation can control ciliary beating, motility, signaling, length, and assembly. Despite the importance of this posttranslational modification, the identities of many ciliary phosphoproteins and knowledge about their in vivo phosphorylation sites are still missing. Here we used immobilized metal affinity chromatography to enrich phosphopeptides from purified flagella and analyzed them by mass spectrometry. One hundred forty-one phosphorylated peptides were identified, belonging to 32 flagellar proteins. Thereby, 126 in vivo phosphorylation sites were determined. The flagellar phosphoproteome includes different structural and motor proteins, kinases, proteins with protein interaction domains, and many proteins whose functions are still unknown. In several cases, a dynamic phosphorylation pattern and clustering of phosphorylation sites were found, indicating a complex physiological status and specific control by reversible protein phosphorylation in the flagellum.
Spliceosomal Proteomics in
Trypanosoma brucei
Reveal New RNA Splicing Factors
Authors: Luz Ambrósio Daniela , Lee Ju Huck , Panigrahi Aswini K. , Nguyen Tu Ngoc , Cicarelli Regina Maria Barretto , Günzl Arthur 
Published: May 2009

ABSTRACT

In trypanosomatid parasites, spliced leader (SL)
trans
splicing is an essential nuclear mRNA maturation step which caps mRNAs posttranscriptionally and, in conjunction with polyadenylation, resolves individual mRNAs from polycistronic precursors. While all trypanosomatid mRNAs are
trans
spliced, intron removal by
cis
splicing is extremely rare and predicted to occur in only four pre-mRNAs.
trans
- and
cis
-splicing reactions are carried out by the spliceosome, which consists of U-rich small nuclear ribonucleoprotein particles (U snRNPs) and of non-snRNP factors. Mammalian and yeast spliceosome complexes are well characterized and found to be associated with up to 170 proteins. Despite the central importance of
trans
splicing in trypanosomatid gene expression, only the core RNP proteins and a few snRNP-specific proteins are known. To characterize the trypanosome spliceosomal protein repertoire, we conducted a proteomic analysis by tagging and tandem affinity-purifying the canonical core RNP protein SmD1 in
Trypanosoma brucei
and by identifying copurified proteins by mass spectrometry. The set of 47 identified proteins harbored nearly all spliceosomal snRNP factors characterized in trypanosomes thus far and 21 proteins lacking a specific annotation. A bioinformatic analysis combined with protein pull-down assays and immunofluorescence microscopy identified 10 divergent orthologues of known splicing factors, including the missing U1-specific protein U1A. In addition, a novel U5-specific, and, as we show, an essential splicing factor was identified that shares a short, highly conserved N-terminal domain with the yeast protein Cwc21p and was thus tentatively named U5-Cwc21. Together, these data strongly indicate that most of the identified proteins are components of the spliceosome.
Chitin in Diatoms and Its Association with the Cell Wall
Authors: Durkin Colleen A. , Mock Thomas , Armbrust E. Virginia 
Published: May 2009

ABSTRACT

Chitin is a globally abundant polymer widely distributed throughout eukaryotes that has been well characterized in only a few lineages. Diatoms are members of the eukaryotic lineage of stramenopiles. Of the hundreds of diatom genera, two produce long fibers of chitin that extrude through their cell walls of silica. We identify and describe here genes encoding putative chitin synthases in a variety of additional diatom genera, indicating that the ability to produce chitin is more widespread and likely plays a more central role in diatom biology than previously considered. Diatom chitin synthases fall into four phylogenetic clades. Protein domain predictions and differential gene expression patterns provide evidence that chitin synthases have multiple functions within a diatom cell.
Thalassiosira pseudonana
possesses six genes encoding three types of chitin synthases. Transcript abundance of the gene encoding one of these chitin synthase types increases when cells resume division after short-term silicic acid starvation and during short-term limitation by silicic acid or iron, two nutrient conditions connected in the environment and known to affect the cell wall. During long-term silicic acid starvation transcript abundance of this gene and one additional chitin synthase gene increased at the same time a chitin-binding lectin localized to the girdle band region of the cell wall. Together, these results suggest that the ability to produce chitin is more widespread in diatoms than previously thought and that a subset of the chitin produced by diatoms is associated with the cell wall.
She3p Possesses a Novel Activity Required for
ASH1
mRNA Localization in
Saccharomyces cerevisiae
Authors: Landers Sharon M. , Gallas Michelle R. , Little Jaime , Long Roy M. 
Published: May 2009

ABSTRACT

Intracellular and intercellular polarity requires that specific proteins be sorted to discreet locations within and between cells. One mechanism for sorting proteins is through RNA localization. In
Saccharomyces cerevisiae
,
ASH1
mRNA localizes to the distal tip of the bud, resulting in the asymmetric sorting of the transcriptional repressor Ash1p.
ASH1
mRNA localization requires four
cis
-acting localization elements and the
trans
-acting factors Myo4p, She3p, and She2p. Myo4p is a type V myosin motor that functions to directly transport
ASH1
mRNA to the bud. She2p is an RNA-binding protein that directly interacts with the
ASH1
mRNA
cis
-acting elements. Currently, the role for She3p in
ASH1
mRNA localization is as an adaptor protein, since it can simultaneously associate with Myo4p and She2p. Here, we present data for two novel mutants of She3p, S348E and the double mutant S343E S361E, that are defective for
ASH1
mRNA localization, and yet both of these mutants retain the ability to associate with Myo4p and She2p. These observations suggest that She3p possesses a novel activity required for
ASH1
mRNA localization, and our data imply that this function is related to the ability of She3p to associate with
ASH1
mRNA. Interestingly, we determined that She3p is phosphorylated, and global mass spectrometry approaches have determined that Ser 343, 348, and 361 are sites of phosphorylation, suggesting that the novel function for She3p could be negatively regulated by phosphorylation. The present study reveals that the current accepted model for
ASH1
mRNA localization does not fully account for the function of She3p in
ASH1
mRNA localization.
The Cell End Marker Protein TeaC Is Involved in Growth Directionality and Septation in
Aspergillus nidulans
Authors: Higashitsuji Yuhei , Herrero Saturnino , Takeshita Norio , Fischer Reinhard 
Published: May 2009

ABSTRACT

Polarized growth in filamentous fungi depends on the correct spatial organization of the microtubule (MT) and actin cytoskeleton. In
Schizosaccharomyces pombe
it was shown that the MT cytoskeleton is required for the delivery of so-called cell end marker proteins, e.g., Tea1 and Tea4, to the cell poles. Subsequently, these markers recruit several proteins required for polarized growth, e.g., a formin, which catalyzes actin cable formation. The latest results suggest that this machinery is conserved from fission yeast to
Aspergillus nidulans.
Here, we have characterized TeaC, a putative homologue of Tea4. Sequence identity between TeaC and Tea4 is only 12.5%, but they both share an SH3 domain in the N-terminal region. Deletion of
teaC
affected polarized growth and hyphal directionality. Whereas wild-type hyphae grow straight, hyphae of the mutant grow in a zig-zag way, similar to the hyphae of
teaA
deletion (
tea1
) strains. Some small, anucleate compartments were observed. Overexpression of
teaC
repressed septation and caused abnormal swelling of germinating conidia. In agreement with the two roles in polarized growth and in septation, TeaC localized to hyphal tips and to septa. TeaC interacted with the cell end marker protein TeaA at hyphal tips and with the formin SepA at hyphal tips and at septa.
3-Hydroxypropionyl-Coenzyme A Dehydratase and Acryloyl-Coenzyme A Reductase, Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in the
Sulfolobales
Authors: Teufel Robin , Kung Johannes W. , Kockelkorn Daniel , Alber Birgit E. , Fuchs Georg 
Published: May 2009

ABSTRACT

A 3-hydroxypropionate/4-hydroxybutyrate cycle operates in autotrophic CO
2
fixation in various
Crenarchaea
, as studied in some detail in
Metallosphaera sedula
. This cycle and the autotrophic 3-hydroxypropionate cycle in
Chloroflexus aurantiacus
have in common the conversion of acetyl-coenzyme A (CoA) and two bicarbonates via 3-hydroxypropionate to succinyl-CoA. Both cycles require the reductive conversion of 3-hydroxypropionate to propionyl-CoA. In
M. sedula
the reaction sequence is catalyzed by three enzymes. The first enzyme, 3-hydroxypropionyl-CoA synthetase, catalyzes the CoA- and MgATP-dependent formation of 3-hydroxypropionyl-CoA. The next two enzymes were purified from
M. sedula
or
Sulfolobus tokodaii
and studied. 3-Hydroxypropionyl-CoA dehydratase, a member of the enoyl-CoA hydratase family, eliminates water from 3-hydroxypropionyl-CoA to form acryloyl-CoA. Acryloyl-CoA reductase, a member of the zinc-containing alcohol dehydrogenase family, reduces acryloyl-CoA with NADPH to propionyl-CoA. Genes highly similar to the
Metallosphaera
CoA synthetase, dehydratase, and reductase genes were found in autotrophic members of the
Sulfolobales
. The encoded enzymes are only distantly related to the respective three enzyme domains of propionyl-CoA synthase from
C. aurantiacus
, where this trifunctional enzyme catalyzes all three reactions. This indicates that the autotrophic carbon fixation cycles in
Chloroflexus
and in the
Sulfolobales
evolved independently and that different genes/enzymes have been recruited in the two lineages that catalyze the same kinds of reactions.