46 research outputs found
Blue-light reception through quaternary transitions
Sensory photoreceptors absorb light via their photosensor modules and trigger
downstream physiological adaptations via their effector modules. Light
reception accordingly depends on precisely orchestrated interactions between
these modules, the molecular details of which often remain elusive. Using
electron-electron double resonance (ELDOR) spectroscopy and site-directed spin
labelling, we chart the structural transitions facilitating blue-light
reception in the engineered light-oxygen-voltage (LOV) histidine kinase YF1
which represents a paradigm for numerous natural signal receptors. Structural
modelling based on pair-wise distance constraints derived from ELDOR pinpoint
light-induced rotation and splaying apart of the two LOV photosensors in the
dimeric photoreceptor. Resultant molecular strain likely relaxes as left-
handed supercoiling of the coiled-coil linker connecting sensor and effector
units. ELDOR data on a photoreceptor variant with an inverted signal response
indicate a drastically altered dimer interface but light-induced structural
transitions in the linker that are similar to those in YF1. Taken together, we
provide mechanistic insight into the signal trajectories of LOV photoreceptors
and histidine kinases that inform molecular simulations and the engineering of
novel receptors
Cellular Metabolites Enhance the Light Sensitivity of Arabidopsis Cryptochrome through Alternate Electron Transfer Pathways
Cryptochromes are blue light receptors with multiple signaling roles in plants
and animals. Plant cryptochrome (cry1 and cry2) biological activity has been
linked to flavin photoreduction via an electron transport chain comprising
three evolutionarily conserved tryptophan residues known as the Trp triad.
Recently, it has been reported that cry2 Trp triad mutants, which fail to
undergo photoreduction in vitro, nonetheless show biological activity in vivo,
raising the possibility of alternate signaling pathways. Here, we show that
Arabidopsis thaliana cry2 proteins containing Trp triad mutations indeed
undergo robust photoreduction in living cultured insect cells. UV/Vis and
electron paramagnetic resonance spectroscopy resolves the discrepancy between
in vivo and in vitro photochemical activity, as small metabolites, including
NADPH, NADH, and ATP, were found to promote cry photoreduction even in mutants
lacking the classic Trp triad electron transfer chain. These metabolites
facilitate alternate electron transfer pathways and increase light-induced
radical pair formation. We conclude that cryptochrome activation is consistent
with a mechanism of light-induced electron transfer followed by flavin
photoreduction in vivo. We further conclude that in vivo modulation by
cellular compounds represents a feature of the cryptochrome signaling
mechanism that has important consequences for light responsivity and
activation
A structural model for the full-length blue light-sensing protein YtvA from Bacillus subtilis, based on EPR spectroscopy
A model for the full-length structure of the blue light-sensing protein YtvA
from Bacillus subtilis has been determined by EPR spectroscopy, performed on
spin labels selectively inserted at amino acid positions 54, 80, 117 and 179.
Our data indicate that YtvA forms a dimer in solution and enable us, based on
the known structures of the individual domains and modelling, to propose a
three-dimensional model for the full length protein. Most importantly, this
includes the YtvA N-terminus that has so far not been identified in any
structural model. We show that our data are in agreement with the crystal
structure of an engineered LOV-domain protein, YF1, that shows the N-terminus
of the protein to be helical and to fold back in between the β-sheets of the
two LOV domains, and argue for an identical arrangement in YtvA. While we
could not detect any structural changes upon blue-light activation of the
protein, this structural model now forms an ideal basis for identifying
residues as targets for further spin labelling studies to detect potential
conformational changes upon irradiation of the protein
Signal transduction in light-oxygen-voltage receptors lacking the adduct- forming cysteine residue
Light–oxygen–voltage (LOV) receptors sense blue light through the
photochemical generation of a covalent adduct between a flavin-nucleotide
chromophore and a strictly conserved cysteine residue. Here we show that,
after cysteine removal, the circadian-clock LOV-protein Vivid still undergoes
light-induced dimerization and signalling because of flavin photoreduction to
the neutral semiquinone (NSQ). Similarly, photoreduction of the engineered LOV
histidine kinase YF1 to the NSQ modulates activity and downstream effects on
gene expression. Signal transduction in both proteins hence hinges on flavin
protonation, which is common to both the cysteinyl adduct and the NSQ. This
general mechanism is also conserved by natural cysteine-less, LOV-like
regulators that respond to chemical or photoreduction of their flavin
cofactors. As LOV proteins can react to light even when devoid of the adduct-
forming cysteine, modern LOV photoreceptors may have arisen from ancestral
redox-active flavoproteins. The ability to tune LOV reactivity through
photoreduction may have important implications for LOV mechanism and
optogenetic applications
Interaction between top-down and bottom-up control in marine food webs
Climate change and resource exploitation have been shown to modify the importance of bottom-up and top-down forces in ecosystems. However, the resulting pattern of trophic control in complex food webs is an emergent property of the system and thus unintuitive. We develop a statistical nondeterministic model, capable of modeling complex patterns of trophic control for the heavily impacted North Sea ecosystem. The model is driven solely by fishing mortality and climatic variables and based on time-series data covering >40 y for six plankton and eight fish groups along with one bird group (>20 y). Simulations show the outstanding importance of top-down exploitation pressure for the dynamics of fish populations. Whereas fishing effects on predators indirectly altered plankton abundance, bottom-up climatic processes dominate plankton dynamics. Importantly, we show planktivorous fish to have a central role in the North Sea food web initiating complex cascading effects across and between trophic levels. Our linked model integrates bottom-up and top-down effects and is able to simulate complex long-term changes in ecosystem components under a combination of stressor scenarios. Our results suggest that in marine ecosystems, pathways for bottom-up and top-down forces are not necessarily mutually exclusive and together can lead to the emergence of complex patterns of control.En prensa9,77
Effort reduction and the large fish indicator: Spatial trends reveal positive impacts of recent European fleet reduction schemes
The large fish indicator (LFI), or ‘proportion of fish greater than 40 cm length in bottom trawl surveys,’ is a frequently debated indicator of Good Environmental Status in European regional seas. How does the LFI respond to changes in fishing pressure? This question is addressed here through analysis of fine-scale spatial trends in the LFI within the North Sea, compared between two periods of contrasting fisheries management: 1983–1999 and 2000–2012, respectively, before and after the onset of the European Union's fleet reduction scheme. Over the entire period, the LFI has decreased in large parts of the North Sea. However, most of the decline was from 1983–1999; since 2000 the LFI has improved in much of the North Sea, especially in UK waters. Comparison with international effort data shows that those western areas where the LFI has improved correspond with regions where otter trawl effort has decreased since 2000 (and previously was highest in the 1990s), and also with decreases in beam trawl effort. This study provides strong support that recent European effort reduction schemes are now beginning to result in an improved ecosystem state as indicated by the regional-scale improvement in the LFI
Measuring Slepton Masses and Mixings at the LHC
Flavor physics may help us understand theories beyond the standard model. In
the context of supersymmetry, if we can measure the masses and mixings of
sleptons and squarks, we may learn something about supersymmetry and
supersymmetry breaking. Here we consider a hybrid gauge-gravity supersymmetric
model in which the observed masses and mixings of the standard model leptons
are explained by a U(1) x U(1) flavor symmetry. In the supersymmetric sector,
the charged sleptons have reasonably large flavor mixings, and the lightest is
metastable. As a result, supersymmetric events are characterized not by missing
energy, but by heavy metastable charged particles. Many supersymmetric events
are therefore fully reconstructible, and we can reconstruct most of the charged
sleptons by working up the long supersymmetric decay chains. We obtain
promising results for both masses and mixings, and conclude that, given a
favorable model, precise measurements at the LHC may help shed light not only
on new physics, but also on the standard model flavor parameters.Comment: 24 pages; v2: fixed a typo in our computer program that led to some
miscalculated branching ratios, various clarifications and minor
improvements, conclusions unchanged, published versio
XPS guide: Charge neutralization and binding energy referencing for insulating samples
This guide deals with methods to control surface charging during XPS analysis of insulating samples and approaches to extracting useful binding energy information. The guide summarizes the causes of surface charging, how to recognize when it occurs, approaches to minimize charge buildup, and methods used to adjust or correct XPS photoelectron binding energies when charge control systems are used. There are multiple ways to control surface charge buildup during XPS measurements, and examples of systems on advanced XPS instruments are described. There is no single, simple, and foolproof way to extract binding energies on insulating material, but advantages and limitations of several approaches are described. Because of the variety of approaches and limitations of each, it is critical for researchers to accurately describe the procedures that have been applied in research reports and publications