120 research outputs found
Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
<p>Abstract</p> <p>Background</p> <p>In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of <it>Nitrosomonas europaea</it>, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family.</p> <p>Results</p> <p>Of the three <it>N. europaea fur </it>homologs, only the Fur homolog encoded by gene NE0616 complemented the <it>Escherichia coli </it>H1780 <it>fur </it>mutant. A <it>N. europaea fur:kanP </it>mutant strain was created by insertion of kanamycin-resistance cassette in the promoter region of NE0616 <it>fur </it>homolog. The total cellular iron contents of the <it>fur:kanP </it>mutant strain increased by 1.5-fold compared to wild type when grown in Fe-replete media. Relative to the wild type, the <it>fur:kanP </it>mutant exhibited increased sensitivity to iron at or above 500 μM concentrations. Unlike the wild type, the <it>fur:kanP </it>mutant was capable of utilizing iron-bound ferrioxamine without any lag phase and showed over expression of several outer membrane TonB-dependent receptor proteins irrespective of Fe availability.</p> <p>Conclusions</p> <p>Our studies have clearly indicated a role in Fe regulation by the Fur protein encoded by <it>N. europaea </it>NE0616 gene. Additional studies are required to fully delineate role of this <it>fur </it>homolog.</p
Ultra-Short-Chain PFASs in the Sources of German Drinking Water: Prevalent, Overlooked, Difficult to Remove, and Unregulated
acceptedVersio
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Acetylene Inhibition of Azotobacter vinelandii Hydrogenase: Acetylene Binds Tightly to the Large Subunit
Acetylene is a slow-binding inhibitor of the Ni- and Fe-containing dimeric hydrogenase isolated
from Azotobacter vinelandii. Acetylene was released from hydrogenase during the recovery from inhibition.
This indicates that no transformation of acetylene to another compound occurred as a result of the interaction
with hydrogenase. However, the release of C2H2 proceeds more rapidly than the recovery of activity, which
indicates that release of C2H2 is not sufficient for recovery of activity. Acetylene binds tightly to native
hydrogenase; hydrogenase and radioactivity cuelute from a gel permeation column following inhibition with
14C2H2A. cetylene, or a derivative, remains bound to the large 65 000 MW subunit (and not to the small
35 000 MW subunit) of hydrogenase following denaturation as evidenced by SDS-PAGE and fluorography
of l4C2H,-inhibited hydrogenase. This result suggests that C2H2, and by analogy H,, binds to and is activated
by the large subunit of this dimeric hydrogenase. Radioactivity is lost from 14C2H,-inhibited protein during
recovery. The inhibition is remarkably specific for C2H2: propyne, butyne, and ethylene are not inhibitors
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Kinetic and Spectroscopic Analysis of the Inactivating Effects of Nitric Oxide on the Individual Components of Azotobacter vinelandii Nitrogenase
The effects of nitric oxide (NO) on the individual components of Azotobacter vinelandii
nitrogenase have been examined by kinetic and spectroscopic methods. Incubation of the Fe protein (Av2)
for 1 h with stoichiometries of 4- and 8-fold molar excesses of NO to Av2 dimer resulted in a complete
loss of activity of Av2 in C2H2-reduction assays. The kinetics of inactivation indicated that the minimum
stoichiometry of NO to Av2 required to fully inactivate Av2 lies between 1 and 2. The rate of inactivation
of Av2 activity by NO was stimulated up to 2-fold by the presence of MgATP and MgADP but was
unaffected by the presence of sodium dithionite. Unexpectedly, complete inactivation of Av2 by low ratios
of NO to Av2 also resulted in a complete loss of its ability to bind MgATP and MgADP. UV-visible
spectroscopy indicated that the effect of NO on Av2 involves oxidation of the [4Fe-4S] center. EPR
spectroscopy revealed that the loss of activity during inactivation of Av2 by NO correlated with the loss
of the S = 1/2 and S = 3/2 signals. Appearance of the classical and intense iron-nitrosyl signal (g = 2.03)
was only observed when Av2 was incubated with large molar excesses of NO and the appearance of this
signal did not correlate with the loss of Av2 activity. The effects of NO on the MoFe protein (Avl) were
more complex than for Av2. A time-dependent inactivation of Avl activity (C2H2 reduction) was observed
which required considerably higher concentrations of NO than those required to inactivate Av2 (up to 10
P a ) . In addition, the effects of NO on Avl were significantly affected by the presence of sodium dithionite.
In fact, kinetic evidence suggests that an Avl-catalyzed, NO-dependent consumption of dithionite occurs
before Avl is inactivated by NO. A correlation between UV-visible and EPR spectral features and the
extent of NO inactivation has been established. The inactivation of either nitrogenase component by NO
did not lead to aggregation or dissolution into their constitutive subunits. However, NO inactivation did
cause changes in both proteins since neither NO-treated protein inhibited C2H2-reducing activity in assays
containing equimolar concentrations of untreated protein. The effects of NO on both nitrogenase components
are interpreted in terms of the known reactivity of NO with Fe-S centers
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Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’
Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex
expressed by the C2–C9 alkane-utilizing bacterium Thauera butanivorans, was kinetically
characterized by measuring substrate specificities for C1–C5 alkanes and product inhibition
profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and
shares a similar substrate range, including gaseous and liquid alkanes, aromatics, alkenes and
halogenated xenobiotics. Results indicated that butane was the preferred substrate (defined by
kcat : Km ratios). Relative rates of oxidation for C1–C5 alkanes differed minimally, implying that
substrate specificity is heavily influenced by differences in substrate Km values. The low
micromolar Km for linear C2–C5 alkanes and the millimolar Km for methane demonstrate that
sBMO is two to three orders of magnitude more specific for physiologically relevant substrates of
T. butanivorans. Methanol, the product of methane oxidation and also a substrate itself, was found
to have similar Km and kcat values to those of methane. This inability to kinetically discriminate
between the C1 alkane and C1 alcohol is observed as a steady-state concentration of methanol
during the two-step oxidation of methane to formaldehyde by sBMO. Unlike methanol, alcohols
with chain length C2–C5 do not compete effectively with their respective alkane substrates.
Results from product inhibition experiments suggest that the geometry of the active site is
optimized for linear molecules four to five carbons in length and is influenced by the regulatory
protein component B (butane monooxygenase regulatory component; BMOB). The data suggest
that alkane oxidation by sBMO is highly specialized for the turnover of C3–C5 alkanes and the
release of their respective alcohol products. Additionally, sBMO is particularly efficient at
preventing methane oxidation during growth on linear alkanes ≥C2, despite its high sequence
homology with sMMO. These results represent, to the best of our knowledge, the first kinetic in
vitro characterization of the closest known homologue of sMM
Triggered Star Formation in Galaxy Pairs at z=0.08-0.38
We measure the strength, frequency, and timescale of tidally triggered star
formation at redshift z=0.08-0.38 in a spectroscopically complete sample of
galaxy pairs drawn from the magnitude-limited redshift survey of 9,825
Smithsonian Hectospec Lensing Survey (SHELS) galaxies with R<20.3. To examine
the evidence for tidal triggering, we identify a volume-limited sample of major
(|\Delta M_R|1/5) pair galaxies with $M_R <
-20.8 in the redshift range z=0.08-0.31. The size and completeness of the
spectroscopic survey allows us to focus on regions of low local density. The
spectrophotometric calibration enables the use of the 4000 Ang break (D_n4000),
the H\alpha specific star formation rate (SSFR_{H\alpha}), and population
models to characterize the galaxies. We show that D_n4000 is a useful
population classification tool; it closely tracks the identification of
emission line galaxies. The sample of major pair galaxies in regions of low
local density with low D_n4000 demonstrates the expected anti-correlation
between pair-wise projected separation and a set of star formation indicators
explored in previous studies. We measure the frequency of triggered star
formation by comparing the SSFR_{H\alpha} in the volume-limited sample in
regions of low local density: 32 +/-7% of the major pair galaxies have
SSFR_{H\alpha} at least double the median rate of the unpaired field galaxies.
Comparison of stellar population models for pair and for unpaired field
galaxies implies a timescale for triggered star formation of ~300-400 Myr.Comment: 25 pages, 15 figures. Accepted to A
Cell density and airspace patterning in the leaf can be manipulated to increase leaf photosynthetic capacity
The pattern of cell division, growth and separation during leaf development determines the pattern and volume of airspace in a leaf. The resulting balance of cellular material and airspace is expected to significantly influence the primary function of the leaf, photosynthesis, and yet the manner and degree to which cell division patterns affect airspace networks and photosynthesis remains largely unexplored. In this paper we investigate the relationship of cell size and patterning, airspace and photosynthesis by promoting and repressing the expression of cell cycle genes in the leaf mesophyll. Using microCT imaging to quantify leaf cellular architecture and fluorescence/gas exchange analysis to measure leaf function, we show that increased cell density in the mesophyll of Arabidopsis can be used to increase leaf photosynthetic capacity. Our analysis suggests that this occurs both by increasing tissue density (decreasing the relative volume of airspace) and by altering the pattern of airspace distribution within the leaf. Our results indicate that cell division patterns influence the photosynthetic performance of a leaf, and that it is possible to engineer improved photosynthesis via this approach
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Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria
Ammonia (NH₃)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH₃ oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤20 μM concentrations of 1-alkynes C₈ and C₉. In contrast, NH₃ oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 μM C₈ (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH₄⁺-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH₄⁺-stimulated net nitrification rates of 2 and 7 μg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 μM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH₄⁺-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Society for Microbiology and can be found at: http://aem.asm.org/
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Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia
Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower K[subscript m]), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide
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