Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study

The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.

A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins

Signal proteins are able to adapt their response to a change in the environment, governing in this way a broad variety of important cellular processes in living systems. While conventional molecular-dynamics (MD) techniques can be used to explore the early signaling pathway of these protein systems at atomistic resolution, the high computational costs limit their usefulness for the elucidation of the multiscale transduction dynamics of most signaling processes, occurring on experimental timescales. To cope with the problem, we present in this paper a novel multiscale-modeling method, based on a combination of the kinetic Monte-Carlo- and MD-technique, and demonstrate its suitability for investigating the signaling behavior of the photoswitch light-oxygen-voltage-2-Jα domain from Avena Sativa (AsLOV2-Jα) and an AsLOV2-Jα-regulated photoactivable Rac1-GTPase (PA-Rac1), recently employed to control the motility of cancer cells through light stimulus. More specifically, we show that their signaling pathways begin with a residual re-arrangement and subsequent H-bond formation of amino acids near to the flavin-mononucleotide chromophore, causing a coupling between β-strands and subsequent detachment of a peripheral α-helix from the AsLOV2-domain. In the case of the PA-Rac1 system we find that this latter process induces the release of the AsLOV2-inhibitor from the switchII-activation site of the GTPase, enabling signal activation through effector-protein binding. These applications demonstrate that our approach reliably reproduces the signaling pathways of complex signal proteins, ranging from nanoseconds up to seconds at affordable computational costs.

Signaling pathway of a photoactivable Rac1-GTPase in the early stages

In modern life- and medical-sciences major efforts are currently concentrated on creating artificial photoenzymes, consisting of light- oxygen-voltage-sensitive (LOV) domains fused to a target enzyme. Such protein constructs possess great potential for controlling the cell metabolism as well as gene function upon light stimulus. This has recently been impressively demonstrated by designing a novel artificial fusion protein, connecting the AsLOV2-Jα-photosensor from Avena sativa with the Rac1-GTPase (AsLOV2-Jα-Rac1), and by using it, to control the motility of cancer cells from the HeLa-line. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their signaling pathway after photoexcitation is still in its infancy. Here, we show through computer simulations of the AsLOV2-Jα-Rac1-photoenzyme that the early processes after formation of the Cys450-FMN-adduct involve the breakage of a H-bond between the carbonyl oxygen FMN-C4O and the amino group of Gln513, followed by a rotational reorientation of its sidechain. This initial event is followed by successive events including β-sheet tightening and transmission of torsional stress along the Iβ-sheet, which leads to the disruption of the Jα-helix from the N-terminal end. Finally, this process triggers the detachment of the AsLOV2-Jα-photosensor from the Rac1-GTPase, ultimately enabling the activation of Rac1 via binding of the effector protein PAK1.

The role of human-induced fire and sweet chestnut (Castanea sativa Mill.) cultivation on the long-term landscape dynamics of the southern Swiss Alps

Changes in fire occurrence during the last decades in the southern Swiss Alps make knowledge on fire history essential to understand future evolution of the ecosystem composition and functioning. In this context, palaeoecology provides useful insights into processes operating at decadal-to-millennial time scales, such as the response of plant communities to intensified fire disturbances during periods of cultural change. We provide a high-resolution macroscopic charcoal and pollen series from Guèr, a well-dated peat sequence at mid-elevation (832 m.a.s.l.) in southern Switzerland, where the presence of local settlements is documented since the late Bronze Age and the Iron Age. Quantitative fire reconstruction shows that fire activity sharply increased from the Neolithic period (1–3 episodes/1000 year) to the late Bronze and Iron Age (7–9 episodes/1000 year), leading to extensive clearance of the former mixed deciduous forest (Alnus glutinosa, Betula, deciduous Quercus). The increase in anthropogenic pollen indicators (e.g. Cerealia-type, Plantago lanceolata) together with macroscopic charcoal suggests anthropogenic rather than climatic forcing as the main cause of the observed vegetation shift. Fire and controlled burning were extensively used during the late Roman Times and early Middle Ages to promote the introduction and establishment of chestnut (Castanea sativa) stands, which provided an important wood and food supply. Fire occurrence declined markedly (from 9 to 5–6 episodes/1000 year) during late Middle Ages because of fire suppression, biomass removal by human population, and landscape fragmentation. Land-abandonment during the last decades allowed forest to partly re-expand (mainly Alnus glutinosa, Betula) and fire frequency to increase.

Castanea sativa in Europe: distribution, habitat, usage and threats

The sweet chestnut (Castanea sativa Mill.) is the only native species of the genus in Europe. The broad diffusion and active management by man resulted in the establishment of the species at the limits of its potential ecological range, which makes it difficult to trace its original natural area. The present distribution ranges from North-Western Africa (e.g. Morocco) to North-Western Europe (southern England, Belgium) and from south-western Asia (e.g. Turkey) to Eastern Europe (e.g. Romania), the Caucasus (Georgia, Armenia) and the Caspian Sea. In Europe the main chestnut forests are concentrated in a few countries such as Italy, France and the Iberian Peninsula. The sweet chestnut has a remarkable multipurpose character, and may be managed for timber production (coppice and high forest) as well as for fruit production (traditional orchards), including a broad range of secondary products and ecosystem services.

Quaternary refugia of the sweet chestnut (Castanea sativa Mill.): an extended palynological approach

Knowledge about the glacial refugia of the thermophilous European Castanea sativa Mill. (sweet chestnut) is still inadequate. Its original range of distribution has been masked by strong human impact. Moreover, under natural conditions the species was probably admixed with other taxa (such as Quercus, Fraxinus, Fagus, Tilia) and thus possibly represented by low percentages in pollen records. In this paper we try to overcome the difficulties related to the scarcity and irregularity of chestnut pollen records by considering 1471 sites and extending the palynological approach to develop a Castanea refugium probability index (IRP), aimed at detecting possible chestnut refugia where chestnuts survived during the last glaciation. The results are in close agreement with the current literature on the refugia of other thermophilous European trees. The few divergences are most probably due to the large amount of new data integrated in this study, rather than to fundamental disagreements about data and data interpretation. The main chestnut refugia are located in the Transcaucasian region, north-western Anatolia, the hinterland of the Tyrrhenian coast from Liguria to Lazio along the Apennine range, the region around Lago di Monticchio (Monte Vulture) in southern Italy, and the Cantabrian coast on the Iberian peninsula. Despite the high likelihood of Castanea refugia in the Balkan Peninsula and north-eastern Italy (Colli Euganei, Monti Berici, Emilia-Romagna) as suggested by the IRP, additional palaeobotanical investigations are needed to assess whether these regions effectively sheltered chestnut during the last glaciation. Other regions, such as the Isère Département in France, the region across north-west Portugal and Galicia, and the hilly region along the Mediterranean coast of Syria and Lebanon were classified as areas of medium refugium probability. Our results reveal an unexpected spatial richness of potential Castanea refugia. It is likely that other European trees had similar distribution ranges during the last glaciation. It is thus conceivable that shelter zones with favourable microclimates were probably more numerous and more widely dispersed across Europe than so far assumed. In the future, more attention should be paid to pollen traces of sporadic taxa thought to have disappeared from a given area during the last glacial and post-glacial period.

The cultivation of Castanea sativa (Mill.) in Europe, from its origin to its diffusion on a continental scale

The history of Castanea sativa (sweet chestnut) cultivation since medieval times has been well described on the basis of the very rich documentation available. Far fewer attempts have been made to give a historical synthesis of the events that led to the cultivation of sweet chestnut in much earlier times. In this article we attempt to reconstruct this part of the European history of chestnut cultivation and its early diffusion by use of different sources of information, such as pollen studies, archaeology, history and literature. Using this multidisciplinary approach, we have tried to identify the roles of the Greek and Roman civilizations in the dissemination of chestnut cultivation on a European scale. In particular, we show that use of the chestnut for food was not the primary driving force behind the introduction of the tree into Europe by the Romans. Apart from the Insubrian Region in the north of the Italian peninsula, no other centre of chestnut cultivation existed in Europe during the Roman period. The Romans may have introduced the idea of systematically cultivating and using chestnut. In certain cases they introduced the species itself; however no evidence of systematic planting of chestnut exists. The greatest interest in the management of chestnut for fruit production most probably developed after the Roman period and can be associated with the socio-economic structures of medieval times. It was then that self-sufficient cultures based on the cultivation of chestnut as a source of subsistence were formed.