bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Autotrophy via the Reverse Tricarboxylic Acid Cycle in the Marine Magnetotactic Coccus Strain MC-1
Authors: Williams Timothy J. , Zhang Chuanlun L. , Scott James H. , Bazylinski Dennis A. 
Published: February 2006

ABSTRACT

Strain MC-1 is a marine, microaerophilic, magnetite-producing, magnetotactic coccus phylogenetically affiliated with the α-
Proteobacteria
. Strain MC-1 grew chemolithotrophically with sulfide and thiosulfate as electron donors with HCO
3
−
/CO
2
as the sole carbon source. Experiments with cells grown microaerobically in liquid with thiosulfate and H
14
CO
3
−
/
14
CO
2
showed that all cell carbon was derived from H
14
CO
3
−
/
14
CO
2
and therefore that MC-1 is capable of chemolithoautotrophy. Cell extracts did not exhibit ribulose-1,5-bisphosphate carboxylase-oxygenase (RubisCO) activity, nor were RubisCO genes found in the draft genome of MC-1. Thus, unlike other chemolithoautotrophic, magnetotactic bacteria, strain MC-1 does not appear to utilize the Calvin-Benson-Bassham cycle for autotrophy. Cell extracts did not exhibit carbon monoxide dehydrogenase activity, indicating that the acetyl-coenzyme A pathway also does not function in strain MC-1. The
13
C content of whole cells of MC-1 relative to the
13
C content of the inorganic carbon source (Δδ
13
C) was −11.4

. Cellular fatty acids showed enrichment of
13
C relative to whole cells. Strain MC-1 cell extracts showed activities for several key enzymes of the reverse (reductive) tricarboxylic acid (rTCA) cycle including fumarate reductase, pyruvate:acceptor oxidoreductase and 2-oxoglutarate:acceptor oxidoreductase. Although ATP citrate lyase (another key enzyme of the rTCA cycle) activity was not detected in strain MC-1 using commonly used assays, cell extracts did cleave citrate, and the reaction was dependent upon the presence of ATP and coenzyme A. Thus, we infer the presence of an ATP-dependent citrate-cleaving mechanism. These results are consistent with the operation of the rTCA cycle in MC-1. Strain MC-1 appears to be the first known representative of the α-
Proteobacteria
to use the rTCA cycle for autotrophy.
Involvement of Two Specific Causes of Cell Mortality in Freeze-Thaw Cycles with Freezing to −196°C
Authors: Dumont Frédéric , Marechal Pierre-André , Gervais Patrick 
Published: February 2006

ABSTRACT
The purpose of this study was to examine cell viability after freezing. Two distinct ranges of temperature were identified as corresponding to stages at which yeast cell mortality occurred during freezing to −196°C. The upper temperature range was related to the temperature of crystallization of the medium, which was dependent on the solute concentration; in this range mortality was prevented by high solute concentrations, and the proportion of the medium in the vitreous state was greater than the proportion in the crystallized state. The lower temperature range was related to recrystallization that occurred during thawing. Mortality in this temperature range was increased by a high cooling rate and/or high solute concentration in the freezing medium and a low temperature (less than −70°C). However, a high rate of thawing prevented yeast mortality in this lower temperature range. Overall, it was found that cell viability could be conserved better under freezing conditions by increasing the osmotic pressure of the medium and by using an increased warming rate.
Several Archaeal Homologs of Putative Oligopeptide-Binding Proteins Encoded byThermotoga maritimaBind Sugars
Authors: Nanavati Dhaval M. , Thirangoon Kamolwan , Noll Kenneth M. 
Published: February 2006

ABSTRACTThe hyperthermophilic bacteriumThermotoga maritimahas shared many genes with archaea through horizontal gene transfer. Several of these encode putative oligopeptide ATP binding cassette (ABC) transporters. We sought to test the hypothesis that these transporters actually transport sugars by measuring the substrate affinities of their encoded substrate-binding proteins (SBPs). This information will increase our understanding of the selective pressures that allowed this organism to retain these archaeal homologs. By measuring changes in intrinsic fluorescence of these SBPs in response to exposure to various sugars, we found that five of the eight proteins examined bind to sugars. We could not identify the ligands of the SBPs TM0460, TM1150, and TM1199. The ligands for the archaeal SBPs are TM0031 (BglE), the β-glucosides cellobiose and laminaribiose; TM0071 (XloE), xylobiose and xylotriose; TM0300 (GloE), large glucose oligosaccharides represented by xyloglucans; TM1223 (ManE), β-1,4-mannobiose; and TM1226 (ManD), β-1,4-mannobiose, β-1,4-mannotriose, β-1,4-mannotetraose, β-1,4-galactosyl mannobiose, and cellobiose. For comparison, seven bacterial putative sugar-binding proteins were examined and ligands for three (TM0595, TM0810, and TM1855) were not identified. The ligands for these bacterial SBPs are TM0114 (XylE), xylose; TM0418 (InoE),myo-inositol; TM0432 (AguE), α-1,4-digalactouronic acid; and TM0958 (RbsB), ribose. We found thatT. maritimadoes not grow on several complex polypeptide mixtures as sole sources of carbon and nitrogen, so it is unlikely that these archaeal ABC transporters are used primarily for oligopeptide transport. Since these SBPs bind oligosaccharides with micromolar to nanomolar affinities, we propose that they are used primarily for oligosaccharide transport.
Unstable Lysogeny and Pseudolysogeny in
Vibrio harveyi
Siphovirus-Like Phage 1
Authors: Khemayan Krit , Pasharawipas Tirasak , Puiprom Orapim , Sriurairatana Siriporn , Suthienkul Orasa , Flegel Timothy W. 
Published: February 2006

ABSTRACT

Exposure of
Vibrio harveyi
(strain VH1114) to
V. harveyi
siphovirus-like phage 1 (VHS1) resulted in the production of a low percentage of lysogenized clones of variable stability. These were retrieved most easily as small colonies within dot plaques. Analysis revealed that VHS1 prophage was most likely carried by VH1114 as an episome rather than integrated into the host chromosome. In the late exponential growth phase, lysogenized VH1114 continuously produced VHS1 but also gave rise to a large number of cured progeny. The absence of phage DNA in the cured progeny was confirmed by the absence of VHS1 DNA in Southern blot and PCR assays. Curiously, these very stable, cured subclones did not show the parental phenotype of clear plaques with VHS1 but instead showed turbid plaques, both in overlaid lawns and in dot plaque assays. This phenotypic difference from the original parental isolate suggested that transient lysogeny by VHS1 had resulted in a stable genetic change in the cured clones. Such clones may be called pseudolysogens (i.e., false lysogens), since they have undergone transient lysogeny and have retained some resistance to full lytic phage development, despite the loss of viable or detectable prophage.
Identification of a
Thiomicrospira denitrificans
-Like Epsilonproteobacterium as a Catalyst for Autotrophic Denitrification in the Central Baltic Sea
Authors: Brettar Ingrid , Labrenz Matthias , Flavier Sébastien , Bötel Julia , Kuosa Harri , Christen Richard , Höfle Manfred G. 
Published: February 2006

ABSTRACT

Identification and functional analysis of key members of bacterial communities in marine and estuarine environments are major challenges for obtaining a mechanistic understanding of biogeochemical processes. In the Baltic Sea basins, as in many other marine environments with anoxic bodies of water, the oxic-anoxic interface is considered a layer of high bacterial turnover of sulfur, nitrogen, and carbon compounds that has a great impact on matter balances in the whole ecosystem. We focused on autotrophic denitrification by oxidation of reduced sulfur compounds as a biogeochemically important process mediating concomitant turnover of sulfur, nitrogen, and carbon. We used a newly developed approach consisting of molecular analyses in stimulation experiments and in situ abundance. The molecular approach was based on single-strand conformational polymorphism (SSCP) analysis of the bacterial community RNA, which allowed identification of potential denitrifiers based on the sequences of enhanced SSCP bands and monitoring of the overall bacterial community during the experiments. Sequences of the SSCP bands of interest were used to design highly specific primers that enabled (i) generation of almost complete 16S rRNA gene sequences using experimental and environmental DNA as templates and (ii) quantification of the bacteria of interest by real-time PCR. By using this approach we identified the bacteria responsible for autotrophic denitrification as a single taxon, an epsilonproteobacterium related to the autotrophic denitrifier
Thiomicrospira denitrificans
. This finding was confirmed by material balances in the experiments that were consistent with those obtained with continuous cultures of
T. denitrificans
. The presence and activity of a bacterium that is phylogenetically and physiologically closely related to
T. denitrificans
could be relevant for the carbon budget of the central Baltic Sea because
T. denitrificans
exhibits only one-half the efficiency for carbon dioxide fixation per mol of sulfide oxidized and mol of nitrate reduced of
Thiobacillus denitrificans
hypothesized previously for this function.
Neutral Lipid Biosynthesis in Engineered
Escherichia coli
: Jojoba Oil-Like Wax Esters and Fatty Acid Butyl Esters
Authors: Kalscheuer Rainer , Stöveken Tim , Luftmann Heinrich , Malkus Ursula , Reichelt Rudolf , Steinbüchel Alexander 
Published: February 2006

ABSTRACT

Wax esters are esters of long-chain fatty acids and long-chain fatty alcohols which are of considerable commercial importance and are produced on a scale of 3 million tons per year. The oil from the jojoba plant (
Simmondsia chinensis
) is the main biological source of wax esters. Although it has a multitude of potential applications, the use of jojoba oil is restricted, due to its high price. In this study, we describe the establishment of heterologous wax ester biosynthesis in a recombinant
Escherichia coli
strain by coexpression of a fatty alcohol-producing bifunctional acyl-coenzyme A reductase from the jojoba plant and a bacterial wax ester synthase from
Acinetobacter baylyi
strain ADP1, catalyzing the esterification of fatty alcohols and coenzyme A thioesters of fatty acids. In the presence of oleate, jojoba oil-like wax esters such as palmityl oleate, palmityl palmitoleate, and oleyl oleate were produced, amounting to up to ca. 1% of the cellular dry weight. In addition to wax esters, fatty acid butyl esters were unexpectedly observed in the presence of oleate. The latter could be attributed to solvent residues of 1-butanol present in the medium component, Bacto tryptone. Neutral lipids produced in recombinant
E. coli
were accumulated as intracytoplasmic inclusions, demonstrating that the formation and structural integrity of bacterial lipid bodies do not require specific structural proteins. This is the first report on substantial biosynthesis and accumulation of neutral lipids in
E. coli
, which might open new perspectives for the biotechnological production of cheap jojoba oil equivalents from inexpensive resources employing recombinant microorganisms.
Comparison of the Efficacies of Disinfectants To Control Microbial Contamination in Dental Unit Water Systems in General Dental Practices across the European Union
Authors: Schel A. J. , Marsh P. D. , Bradshaw D. J. , Finney M. , Fulford M. R. , Frandsen E. , Østergaard E. , ten Cate J. M. , Moorer W. R. , Mavridou A. , Kamma J. J. , Mandilara G. , Stösser L. , Kneist S. , Araujo R. , Contreras N. , Goroncy-Bermes P. , O'Mullane D. , Burke F. , O'Reilly P. , Hourigan G. , O'Sullivan M. , Holman R. , Walker J. T. 
Published: February 2006

ABSTRACTWater delivered by dental unit water systems (DUWS) in general dental practices can harbor high numbers of bacteria, including opportunistic pathogens. Biofilms on tubing within DUWS provide a reservoir for microorganisms and should be controlled. This study compared disinfection products for their ability to meet the American Dental Association's guideline of <200 CFU · ml−1for DUWS water. Alpron, BioBlue, Dentosept, Oxygenal, Sanosil, Sterilex Ultra, and Ster4Spray were tested in DUWS (n= 134) in Denmark, Germany, Greece, Ireland, The Netherlands, Spain, and the United Kingdom. Weekly water samples were tested for total viable counts (TVCs) on yeast extract agar, and, where possible, the effects of products on established biofilm (TVCs) were measured. A 4- to 5-week baseline measurement period was followed by 6 to 8 weeks of disinfection (intermittent or continuous product application). DUWS water TVCs before disinfection ranged from 0 to 5.41 log CFU · ml−1. Disinfectants achieved reductions in the median water TVC ranging from 0.69 (Ster4Spray) to 3.11 (Dentosept) log CFU · ml−1, although occasional high values (up to 4.88 log CFU · ml−1) occurred with all products. Before treatment, 64% of all baseline samples exceeded American Dental Association guidelines, compared to only 17% following commencement of treatment; where tested, biofilm TVCs were reduced to below detectable levels. The antimicrobial efficacies of products varied (e.g., 91% of water samples from DUWS treated with Dentosept or Oxygenal met American Dental Association guidelines, compared to 60% of those treated with Ster4Spray). Overall, the continuously applied products performed better than those applied intermittently. The most effective products were Dentosept and Oxygenal, although Dentosept gave the most consistent and sustained antimicrobial effect over time.
Glutamate Dehydrogenase Activity Can Be Transmitted Naturally to
Lactococcus lactis
Strains To Stimulate Amino Acid Conversion to Aroma Compounds
Authors: Tanous Catherine , Chambellon Emilie , Le Bars Dominique , Delespaul Gilbert , Yvon Mireille 
Published: February 2006

ABSTRACT

Amino acid conversion to aroma compounds by
Lactococcus lactis
is limited by the low production of α-ketoglutarate that is necessary for the first step of conversion. Recently, glutamate dehydrogenase (GDH) activity that catalyzes the reversible glutamate deamination to α-ketoglutarate was detected in
L. lactis
strains isolated from a vegetal source, and the gene responsible for the activity in
L. lactis
NCDO1867 was identified and characterized. The gene is located on a 70-kb plasmid also encoding cadmium resistance. In this study,
gdh
gene inactivation and overexpression confirmed the direct impact of GDH activity of
L. lactis
on amino acid catabolism in a reaction medium at pH 5.5, the pH of cheese. By using cadmium resistance as a selectable marker, the plasmid carrying
gdh
was naturally transmitted to another
L. lactis
strain by a mating procedure. The transfer conferred to the host strain GDH activity and the ability to catabolize amino acids in the presence of glutamate in the reaction medium. However, the plasmid appeared unstable in a strain also containing the protease lactose plasmid pLP712, indicating an incompatibility between these two plasmids.
Degradation of 2,3-Diethyl-5-Methylpyrazine by a Newly Discovered Bacterium,
Mycobacterium
sp. Strain DM-11
Authors: Rappert Sugima , Botsch Kathrin Caroline , Nagorny Stephanie , Francke Wittko , Müller Rudolf 
Published: February 2006

ABSTRACT

A bacterium was isolated from the waste gas treatment plant at a fishmeal processing company on the basis of its capacity to use 2,3-diethyl-5-methylpyrazine (DM) as a sole carbon and energy source. The strain, designated strain DM-11, grew optimally at 25°C and had a doubling time of 29.2 h. The strain did not grow on complex media like tryptic soy broth, Luria-Bertani broth, or nutrient broth or on simple carbon sources like glucose, acetate, oxoglutarate, succinate, or citrate. Only on Löwenstein-Jensen medium was growth observed. The 16S rRNA gene sequence of strain DM-11 showed the highest similarity (96.2%) to
Mycobacterium poriferae
strain ATCC 35087
T
. Therefore, strain DM-11 merits recognition as a novel species within the genus
Mycobacterium.
DM also served as a sole nitrogen source for the growth of strain DM-11. The degradation of DM by strain DM-11 requires molecular oxygen. The first intermediate was identified as 5,6-diethyl-2-hydroxy-3-methylpyrazine (DHM). Its disappearance was accompanied by the release of ammonium into the culture medium. No other metabolite was detected. We conclude that ring fission occurred directly after the formation of DHM and ammonium was eliminated after ring cleavage. Molecular oxygen was essential for the degradation of DHM. The expression of enzymes involved in the degradation of DM and DHM was regulated. Only cells induced by DM or DHM converted these compounds. Strain DM-11 also grew on 2-ethyl-5(6)-methylpyrazine (EMP) and 2,3,5-trimethylpyrazine (TMP) as a sole carbon, nitrogen, and energy source. In addition, the strain converted many pyrazines found in the waste gases of food industries cometabolically.
Phosphorus Scavenging in the Unicellular Marine Diazotroph
Crocosphaera watsonii
Authors: Dyhrman Sonya T. , Haley Sheean T. 
Published: February 2006

ABSTRACT

Through the fixation of atmospheric nitrogen and photosynthesis, marine diazotrophs play a critical role in the global cycling of nitrogen and carbon.
Crocosphaera watsonii
is a recently described unicellular diazotroph that may significantly contribute to marine nitrogen fixation in tropical environments. One of the many factors that can constrain the growth and nitrogen fixation rates of marine diazotrophs is phosphorus bioavailability. Using genomic and physiological approaches, we examined phosphorus scavenging mechanisms in strains of
C. watsonii
from both the Atlantic and the Pacific. Observations from the
C. watsonii
WH8501 genome suggest that this organism has the capacity for high-affinity phosphate transport (e.g., homologs of
pstSCAB
) in low-phosphate, oligotrophic systems. The
pstS
gene (high-affinity phosphate binding) is present in strains isolated from both the Atlantic and the Pacific, and its expression was regulated by the exogenous phosphate supply in strain WH8501. Genomic observation also indicated a broad capacity for phosphomonoester hydrolysis (e.g., a putative alkaline phosphatase). In contrast, no clear homologs of genes for phosphonate transport and hydrolysis could be identified. Consistent with these genomic observations,
C. watsonii
WH8501 is able to grow on phosphomonoesters as a sole source of added phosphorus but not on the phosphonates tested to date. Taken together these data suggest that
C. watsonii
has a robust capacity for scavenging phosphorus in oligotrophic systems, although this capacity differs from that of other marine cyanobacterial genera, such as
Synechococcus
,
Prochlorococcus
, and
Trichodesmium
.
Production of the Lantibiotic Salivaricin A and Its Variants by Oral Streptococci and Use of a Specific Induction Assay To Detect Their Presence in Human Saliva
Authors: Wescombe Philip A. , Upton Mathew , Dierksen Karen P. , Ragland Nancy L. , Sivabalan Senthuran , Wirawan Ruth E. , Inglis Megan A. , Moore Chris J. , Walker Glenn V. , Chilcott Chris N. , Jenkinson Howard F. , Tagg John R. 
Published: February 2006

ABSTRACT

Salivaricin A (SalA), the first
Streptococcus salivarius
lantibiotic to be characterized, appears to be inhibitory to most
Streptococcus pyogenes
strains. A variant of the SalA structural gene (
salA1
) is present in more than 90% of
S. pyogenes
strains, but only strains of M serotype 4 and T pattern 4 produce the biologically active peptide. The present study identifies four additional variants (
salA2
to
salA5
) of the SalA structural gene and demonstrates that each of the corresponding inhibitory peptides (SalA2 to SalA5) is produced in vitro. These variants appear to be similar to SalA and SalA1 in their inhibitory activity against
Micrococcus luteus
and in their ability to act as inducers of SalA production. It had previously been shown that
S. pyogenes
strain SF370 had a deletion (of approximately 2.5 kb) in the
salM
and
salT
genes of the
salA1
locus. In the present study, several additional characteristic deletions within the
salA1
loci were identified.
S. pyogenes
strains of the same M serotype all share the same
salA1
locus structure. Since
S. salivarius
is a predominant member of the normal oral flora of healthy humans, strains producing anti-
S. pyogenes
lantibiotics, such as SalA, may have excellent potential for use as oral probiotics. In the present study, we have used a highly specific SalA induction system to directly detect the presence of SalA in the saliva of humans who either naturally harbor populations of SalA-producing
S. salivarius
or who have been colonized with the SalA2-producing probiotic
S. salivarius
K12.
A Novel
Bacteroidetes
Symbiont Is Localized in
Scaphoideus titanus
, the Insect Vector of Flavescence Dorée in
Vitis vinifera
Authors: Marzorati Massimo , Alma Alberto , Sacchi Luciano , Pajoro Massimo , Palermo Simona , Brusetti Lorenzo , Raddadi Noura , Balloi Annalisa , Tedeschi Rosemarie , Clementi Emanuela , Corona Silvia , Quaglino Fabio , Bianco Piero Attilio , Beninati Tiziana , Bandi Claudio , Daffonchio Daniele 
Published: February 2006

ABSTRACT

Flavescence dorée (FD) is a grapevine disease that afflicts several wine production areas in Europe, from Portugal to Serbia. FD is caused by a bacterium, “
Candidatus
Phytoplasma vitis,” which is spread throughout the vineyards by a leafhopper,
Scaphoideus titanus
(Cicadellidae). After collection of
S. titanus
specimens from FD-contaminated vineyards in three different areas in the Piedmont region of Italy, we performed a survey to characterize the bacterial microflora associated with this insect. Using length heterogeneity PCR with universal primers for bacteria we identified a major peak associated with almost all of the individuals examined (both males and females). Characterization by denaturing gradient gel electrophoresis confirmed the presence of a major band that, after sequencing, showed a 97 to 99% identity with
Bacteroidetes
symbionts of the “
Candidatus
Cardinium hertigii” group. In addition, electron microscopy of tissues of
S. titanus
fed for 3 months on phytoplasma-infected grapevine plants showed bacterial cells with the typical morphology of “
Ca.
Cardinium hertigii.” This endosymbiont, tentatively designated ST1-C, was found in the cytoplasm of previtellogenic and vitellogenic ovarian cells, in the follicle cells, and in the fat body and salivary glands. In addition, cell morphologies resembling those of “
Ca.
Phytoplasma vitis” were detected in the midgut, and specific PCR assays indicated the presence of the phytoplasma in the gut, fat body and salivary glands. These results indicate that ST1-C and “
Ca.
Phytoplasma vitis” have a complex life cycle in the body of
S. titanus
and are colocalized in different organs and tissues.