Evidence for a new metal in a known active site: purification and characterization of an iron-containing quercetin 2,3-dioxygenase from Bacillus subtilis

The protein YxaG from Bacillus subtilis, of previously unknown function, was found to have quercetin 2,3-dioxygenase activity when overexpressed in Escherichia coli. The enzyme converts the flavonol quercetin to 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide, indicating that it performs the same reaction and yields the same products as the well-characterized copper-containing quercetin 2,3-dioxygenase from Aspergillus. In contrast to the Aspergillus protein, YxaG contains iron, and the enzyme is sensitive to strong Fe(II) chelators, similar to the extensively studied catechol dioxygenases. The active site metal was probed by EPR spectroscopy using the label nitric oxide to confirm the presence of an Fe(II) atom. The kinetic parameters and pH activity profiles are also markedly different from those of the copper-containing quercetin 2,3-dioxygenases from Aspergillus. YxaG represents the first example of a prokaryotic quercetin 2,3-dioxygenase.     

Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis

Quercetin 2,3-dioxygenase from Bacillus subtilis (QueD) converts the flavonol quercetin and molecular oxygen to 2-protocatechuoylphloroglucinolcarboxylic acid and carbon monoxide. QueD, the only known quercetin 2,3-dioxygenase from a prokaryotic organism, has been described as an Fe2+-dependent bicupin dioxygenase. Metal-substituted QueDs were generated by expressing the enzyme in Escherichia coli grown on minimal media in the presence of a number of divalent metals. The addition of Mn2+, Co2+, and Cu2+ generated active enzymes, but the addition of Zn2+, Fe2+, and Cd2+ did not increase quercetinase activity to any significant level over a control in which no divalent ions were added to the media. The Mn2+- and Co2+-containing QueDs were purified, characterized by metal analysis and EPR spectroscopy, and studied by steady-state kinetics. Mn2+ was found to be incorporated nearly stoichiometrically to the two cupin motifs. The hyperfine coupling constant of the g = 2 signal in the EPR spectra of the Mn2+-containing enzyme showed that the two Mn2+ ions are ligated in an octahedral coordination. The turnover number of this enzyme was found to be in the order of 25 s(-1), nearly 40-fold higher than that of the Fe2+-containing enzyme and similar in magnitude to that of the Cu2+-containing quercertin 2,3-dioxygenase from Aspergillus japonicus. In addition, kinetic and spectroscopic data suggest that the catalytic mechanism of QueD is different from that of the Aspergillus quercetinases but similar to that proposed for the extradiol catechol dioxygenases. This study provides evidence that Mn2+ might be the preferred cofactor for this enzyme and identifies QueD as a new member of the manganese dioxygenase family.     

Novel regulatory mechanisms for generation of the soluble leptin receptor: implications for leptin action

Background

The adipokine leptin realizes signal transduction via four different membrane-anchored leptin receptor (Ob-R) isoforms in humans. However, the amount of functionally active Ob-R is affected by constitutive shedding of the extracellular domain via a so far unknown mechanism. The product of the cleavage process the so-called soluble leptin receptor (sOb-R) is the main binding protein for leptin in human blood and modulates its bioavailability. sOb-R levels are differentially regulated in metabolic disorders like type 1 diabetes mellitus or obesity and can, therefore, enhance or reduce leptin sensitivity.

Methodology/Principal Findings

To describe mechanisms of Ob-R cleavage and to investigate the functional significance of differential sOb-R levels we established a model of HEK293 cells transiently transfected with different human Ob-R isoforms. Using siRNA knockdown experiments we identified ADAM10 (A Disintegrin And Metalloproteinase 10) as a major protease for constitutive and activated Ob-R cleavage. Additionally, the induction of lipotoxicity and apoptosis led to enhanced shedding shown by increased levels of the soluble leptin receptor (sOb-R) in cell supernatants. Conversely, high leptin concentrations and ER stress reduced sOb-R levels. Decreased amounts of sOb-R due to ER stress were accompanied by impaired leptin signaling and reduced leptin binding.

Conclusions

Lipotoxicity and apoptosis increased Ob-R cleavage via ADAM10-dependent mechanisms. In contrast high leptin levels and ER stress led to reduced sOb-R levels. While increased sOb-R concentrations seem to directly block leptin action, reduced amounts of sOb-R may reflect decreased membrane expression of Ob-R. These findings could explain changes of leptin sensitivity which are associated with variations of serum sOb-R levels in metabolic diseases.     

Human impact diminishes seedling species richness in Kakamega Forest, Kenya

Anthropogenic forest fragmentation and other kinds of human disturbance, such as selective logging, can reduce the diversity of plant and animal species. To evaluate the impact of fragmentation and small-scale disturbance on forest regeneration, we assessed species richness and total abundance of adult trees in comparison with seedlings in the heavily fragmented and disturbed Kakamega Forest, western Kenya. In nine differently disturbed 1-ha study blocks distributed across the main forest and fragments, we mapped all trees >10 cm in diameter at breast height. Additionally, we established ninety 1-m² seedling plots within these 1-ha study blocks which were monitored over 2.5 years. We recorded altogether 74 species of adult trees (30–43 per block) and 64 seedling species (24–41 per block). Neither fragmentation nor small-scale disturbance had an impact on adult tree species richness or total tree abundance. Yet, fragmentation and especially small-scale disturbance significantly reduced seedling species richness, particularly of late-successional species. While human impact did not affect diversity of adults, the impoverished species richness of seedlings suggests a reduced potential for regeneration and a loss of tree diversity in the long-term.     

Assessing fragmentation and disturbance of west Kenyan rainforests by means of remotely sensed time series data and landscape metrics

Biodiversity in tropical rainforests is heavily influenced by land use/cover change (LUCC), but so far there have been few LUCC studies conducted in Africa. We present several methods that make use of remotely sensed data and landscape metrics and allow for assessment of the development of land cover and thus forest fragmentation and disturbance over a substantial period of time. The study covers Kakamega Forest and its associated forest areas in western Kenya, over the last 30 years. The accuracy of a supervised multispectral classification of Landsat time series data encompassing seven time steps between 1972 and 2001 is numerically assessed using ground truth reference data considering the 2001 time step. Here, buffering the forest areas by 1 km, highest user's accuracies for the forest classes ‘near natural + old secondary forest’ (87.50%), ‘secondary forest’ (80.00%) and ‘bushland/shrubs’ (81.08%) are revealed. Images of a spatially distributed fragmentation index derived from the land cover time series by applying a three by 3 pixel‐sized moving window to determine forest pixels’ adjacency, highlight trends in forest fragmentation, e.g. the splitting into two separate forests along the Yala/Ikuywa corridor. Calculations of mean fragmentation indices for the Biodiversity Monitoring Transect Analysis in Eastern Africa (BIOTA‐East Africa) focus research areas are used to evaluate the fragmentation index and to demonstrate its potential to extrapolate (e.g. biological) field findings in space and time. Here we argue for a correlation of the fragmentation indices results not only with forest management regimes, but with population distribution and accessibility (e.g. by roads). A cluster analysis applying the isodata‐algorithm on the classification results of all seven times steps allows for a rapid visual assessment of the distinct pattern of typical land cover development trends since 1972. This reveals that parts of Kakamega Forest have experienced severe forest loss while others, especially in the north‐east, show signs of succession.     

Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib

Multivariate biomarkers that can predict the effectiveness of targeted therapy in individual patients are highly desired. Previous biomarker discovery studies have largely focused on the identification of single biomarker signatures, aimed at maximizing prediction accuracy. Here, we present a different approach that identifies multiple biomarkers by simultaneously optimizing their predictive power, number of features, and proximity to the drug target in a protein-protein interaction network. To this end, we incorporated NSGA-II, a fast and elitist multi-objective optimization algorithm that is based on the principle of Pareto optimality, into the biomarker discovery workflow. The method was applied to quantitative phosphoproteome data of 19 non-small cell lung cancer (NSCLC) cell lines from a previous biomarker study. The algorithm successfully identified a total of 77 candidate biomarker signatures predicting response to treatment with dasatinib. Through filtering and similarity clustering, this set was trimmed to four final biomarker signatures, which then were validated on an independent set of breast cancer cell lines. All four candidates reached the same good prediction accuracy (83%) as the originally published biomarker. Although the newly discovered signatures were diverse in their composition and in their size, the central protein of the originally published signature — integrin β4 (ITGB4) — was also present in all four Pareto signatures, confirming its pivotal role in predicting dasatinib response in NSCLC cell lines. In summary, the method presented here allows for a robust and simultaneous identification of multiple multivariate biomarkers that are optimized for prediction performance, size, and relevance.     

Forest fragmentation and selective logging have inconsistent effects on multiple animal-mediated ecosystem processes in a tropical forest

Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants.