Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity

The protein FkpA from the periplasm of Escherichia coli exhibits both cis/trans peptidyl-prolyl isomerase (PPIase) and chaperone activities. The crystal structure of the protein has been determined in three different forms: as the full-length native molecule, as a truncated form lacking the last 21 residues, and as the same truncated form in complex with the immunosuppressant ligand, FK506. FkpA is a dimeric molecule in which the 245-residue subunit is divided into two domains. The N-terminal domain includes three helices that are interlaced with those of the other subunit to provide all inter-subunit contacts maintaining the dimeric species. The C-terminal domain, which belongs to the FK506-binding protein (FKBP) family, binds the FK506 ligand. The overall form of the dimer is V-shaped, and the different crystal structures reveal a flexibility in the relative orientation of the two C-terminal domains located at the extremities of the V. The deletion mutant FkpNL, comprising the N-terminal domain only, exists in solution as a mixture of monomeric and dimeric species, and exhibits chaperone activity. By contrast, a deletion mutant comprising the C-terminal domain only is monomeric, and although it shows PPIase activity, it is devoid of chaperone function. These results suggest that the chaperone and catalytic activities reside in the N and C-terminal domains, respectively. Accordingly, the observed mobility of the C-terminal domains of the dimeric molecule could effectively adapt these two independent folding functions of FkpA to polypeptide substrates.     

An in silico canine cardiac midmyocardial action potential duration model as a tool for early drug safety assessment

Cell lines expressing ion channels (IC) and the advent of plate-based electrophysiology device have enabled a molecular understanding of the action potential (AP) as a means of early QT assessment. We sought to develop an in silico AP (isAP) model that provides an assessment of the effect of a compound on the myocyte AP duration (APD) using concentration-effect curve data from a panel of five ICs (hNav1.5, hCav1.2, hKv4.3/hKChIP2.2, hKv7.1/hminK, hKv11.1). A test set of 53 compounds was selected to cover a range of selective and mixed IC modulators that were tested for their effects on optically measured APD. A threshold of >10% change in APD at 90% repolarization (APD(90)) was used to signify an effect at the top test concentration. To capture the variations observed in left ventricular midmyocardial myocyte APD data from 19 different dogs, the isAP model was calibrated to produce an ensemble of 19 model variants that could capture the shape and form of the APs and also quantitatively replicate dofetilide- and diltiazem-induced APD(90) changes. Provided with IC panel data only, the isAP model was then used, blinded, to predict APD(90) changes greater than 10%. At a simulated concentration of 30 μM and based on a criterion that six of the variants had to agree, isAP prediction was scored as showing greater than 80% predictivity of compound activity. Thus, early in drug discovery, the isAP model allows integrating separate IC data and is amenable to the throughput required for use as a virtual screen.     

Mathematical modeling of metabolism and hemodynamics

We provide a mathematical study of a model of energy metabolism and hemodynamics of glioma allowing a better understanding of metabolic modifications leading to anaplastic transformation from low grade glioma. This mathematical analysis allows ultimately to unveil the solution to a viability problem which seems quite pertinent for applications to medecine.     

Characterization of the first angiotensin-converting like enzyme in bacteria: Ancestor ACE is already active

Angiotensin-converting enzyme (ACE) is a metallopeptidase that converts angiotensin I into angiotensin II. ACE is crucial in the control of cardiovascular and renal homeostasis and fertility in mammals. In vertebrates, both transmembrane and soluble ACE, containing one or two active sites, have been characterized. So far, only soluble, single domain ACEs from invertebrates have been cloned, and these have been implicated in reproduction in insects. Furthermore, an ACE-related carboxypeptidase was recently characterized in Leishmania, a unicellular eukaryote, suggesting the existence of ACE in more distant organisms. Interestingly, in silico databank analysis revealed that bacterial DNA sequences could encode putative ACE-like proteins, strikingly similar to vertebrates' enzymes. To gain more insight into the bacterial enzymes, we cloned the putative ACE from the phytopathogenic bacterium, Xanthomonas axonopodis pv. citri, named XcACE. The 2 kb open reading frame encodes a 672-amino-acid soluble protein containing a single active site. In vitro expression and biochemical characterization revealed that XcACE is a functional 72 kDa dipeptidyl-carboxypeptidase. As in mammals, this metalloprotease hydrolyses angiotensin I into angiotensin II. XcACE is sensitive to ACE inhibitors and chloride ions concentration. Variations in the active site residues, highlighted by structural modelling, can account for the different substrate selectivity and inhibition profile compared to human ACE. XcACE characterization demonstrates that ACE is an ancestral enzyme, provoking questions about its appearance and structure/activity specialisation during the course of evolution.     

FAK competes for Src to promote migration against invasion in melanoma cells

Melanoma is one of the most deadly cancers because of its high propensity to metastasis, a process that requires migration and invasion of tumor cells driven by the regulated formation of adhesives structures like focal adhesions (FAs) and invasive structures like invadopodia. FAK, the major kinase of FAs, has been implicated in many cellular processes, including migration and invasion. In this study, we investigated the role of FAK in the regulation of invasion. We report that suppression of FAK in B16F10 melanoma cells led to increased invadopodia formation and invasion through Matrigel, but impaired migration. These effects are rescued by FAK WT but not by FAK^Y397F reexpression. Invadopodia formation requires local Src activation downstream of FAK and in a FAK phosphorylation-dependant manner. FAK deletion correlates with increased phosphorylation of Tks-5 (tyrosine kinase substrate with five SH3 domain) and reactive oxygen species production. In conclusion, our data show that FAK is able to mediate opposite effects on cell migration and invasion. Accordingly, beneficial effects of FAK inhibition are context dependent and may depend on the cell response to environmental cues and/or on the primary or secondary changes that melanoma experienced through the invasion cycle.Patients with spreading melanoma diseases have a very poor prognosis with a 5-year survival rate <5%. The metastatic spread of melanoma is a complex process involving several genetic alterations. In melanoma,¹ as in many highly invasive cancer cell types like head and neck squamous cell carcinoma² or breast carcinoma,³ specialized matrix-degrading organelles termed invadopodia have been identified. Invadopodia consist of dynamic actin-based protrusions of 0, 1 to 2 μm in diameter emanating from the ventral edge of tumor cells.⁴ Besides their actin scaffold, these structures are enriched in proteolytic enzymes such as matrix metalloproteinases (MMPs), which mediate extracellular matrix (ECM) degradation. Indeed, MMP are upregulated in invasive melanoma and there is extensive evidence that they have a role in promoting the dissemination of melanoma.^{5, 6, 7} Several proteins like integrins, Src and paxillin, found at sites of cell adhesion to the matrix, are also present in invadopodia.^{8, 9} On the other hand, other proteins like the Src substrate proteins cortactin¹⁰ and the tyrosine kinase substrate with five SH3 domain (Tks-5)¹¹ are specifically localized at invadopodia and not found at focal adhesion (FA). In addition, reactive oxygen species (ROS)¹² have been localized at invadopodia and are supposed to have a prominent role in inducing invadopodia function.^{13, 14} Although significant efforts have been made to characterize components of invadopodia, the precise mechanisms of their regulation, especially in a melanoma context, remain poorly understood.Tumor invasion is a multistep process that requires cell adhesion to the environing substratum, migration and invasion. In many cell types, migration requires fine control of FA turn-over. FAs are formed by the cluster of up to 200 proteins¹⁵ ensuring cell anchorage to the ECM. The cyclic process of FA formation and disruption is crucial for cell migration. Because both anchorage and migration involve cellular interactions with ECM components, FAs are endowed with transmembrane ECM receptor proteins such as integrins that interact with ECM molecules and intra-cellular proteins composed of scaffold proteins, as well as signal-transducing molecules. Among those, focal adhesion kinase (FAK) is a crucial signaling protein that integrates signals from integrins to the actin filaments during cell migration.¹⁶ Structurally, FAK is a 125-kDa protein that contains an N-terminal 4.1-ezrin–radixin–moesin domain, a central kinase domain and a C-terminal domain that contains the focal adhesion targeting site.¹⁷ The phosphorylation of FAK at Y397 creates a binding site for Src, which can phosphorylate other tyrosines on the FAK sequence, thus creating new binding sites for SH2 domain-containing proteins.FAK is involved in many aspects of the metastatic process and thus, overexpression, hyperphosphorylation and/or elevated activity of FAK have been reported in a variety of human cancers, including sarcomas and carcinomas of the breast, colon, thyroid, prostate, oral cavity, liver, stomach and ovary.¹⁸ In human melanoma cell lines, early studies reported high FAK expression and requirement of FAK for cell substrate adhesion.¹⁹ Later, it was reported that FAK promotes the aggressive melanoma phenotype.²⁰ Indeed, immunohistochemical analyses revealed high levels of FAK phosphorylation at Tyr397 and Tyr576, a marker of FAK kinase activity, in late-stage cutaneous and uveal melanoma, which correlated with their increased invasion and migration properties.²¹ Furthermore, melanoma differentiation-associated gene-9 (mda-9)/syntenin was also reported to mediate adhesion-dependant activation of protein kinase Cα (PKCα) and FAK in melanoma cells. Thus, inhibiting either mda-9/syntenin or PKCα suppressed fibronectin-induced formation of integrin-β1/FAK/c-Src signaling complexes and reduced migration and invasion toward fibronectin.²² Therefore, FAK appears to be a major player of melanoma invasion, but how this kinase controls the formation and proteolytic activity of invadopodia in melanoma cells was never investigated.In this study, we uncovered a surprising negative regulation of invadopodia activity in B16F10 cells by FAK. The depletion of FAK was associated with increased ROS production and Tks-5 phosphorylation. Using mutation of FAK at Tyr397, a binding site for Src, we found that these sites are implicated in FAK-mediated inhibition of invadopodia activity. In addition, we report that this mutation induced decreased migration speed but increased invasive properties. Taken together, our data suggest a competition between FA and invadopodia substrates for Src phosphorylation that might depend on environmental cues, thus leading to the engagement of either migration or degradation pathways.     

Molecular cytogenetic characterization of a constitutional complex intrachromosomal 4q rearrangement in a patient with multiple congenital anomalies

Constitutional Complex Chromosomal Rearrangements (CCRs) are very rare. While the vast majority of CCRs involve more than one chromosome, only seven cases describe CCRs with four or more breakpoints within a single chromosome. Here, we present a patient with multiple congenital anomalies and mental retardation. Array Comparative Genomic Hybridisation (array CGH), FISH and Multicolour Banding FISH revealed a de novo complex rearrangement with two deletions, a duplication and an inversion of 4q. This CCR involving at least seven breakpoints is one of the most complex rearrangements of a single chromosome reported thus far. Potential mechanisms generating such complex rearrangements are discussed.     

Taxa distribution and RAPD markers indicate different origin and regional differentiation of hybrids in the invasive Fallopia complex in central-western Europe

Interspecific hybridization can be a driving force for evolutionary processes during plant invasions, by increasing genetic variation and creating novel gene combinations, thereby promoting genetic differentiation among populations of invasive species in the introduced range. We examined regional genetic structure in the invasive Fallopia complex, consisting of F. japonica var. japonica , F.   sachalinensis and their hybrid F.  ×  bohemica , in seven regions in Germany and Switzerland using RAPD analysis and flow cytometry. All individuals identified as F. japonica var . japonica had the same RAPD phenotype, while F. sachalinensis (11 RAPD phenotypes for 11 sampled individuals) and F.  ×  bohemica (24 RAPD phenotypes for 32 sampled individuals) showed high genotypic diversity. Bayesian cluster analysis revealed three distinct genetic clusters. The majority of F . ×  bohemica individuals were assigned to a unique genetic cluster that differed from those of the parental species, while the other F . ×  bohemica individuals had different degrees of admixture to the three genetic clusters. At the regional scale, the occurrence of male-fertile F. sachalinensis coincided with the distribution of F . ×  bohemica plants showing a high percentage of assignment to both parental species, suggesting that they originated from hybridization between the parental species. In contrast, in regions where male-fertile F. sachalinensis were absent, F . ×  bohemica belonged to the non-admixed genetic group, indicating multiple introductions of hybrids or sexual reproduction among hybrids. We also found regional differentiation in the gene pool of F.  ×  bohemica , with individuals within the same region more similar to each other than to individuals from different regions.     

Process-based modelling of isoprene emission by oak leaves

The emission rate of the volatile reactive compound isoprene, emitted predominantly by trees, must be known before the level of photo‐oxidants produced during summer smog can be predicted reliably. The emission is dependent on plant species and local conditions, and these dependencies must be quantified to be included in any empirical algorithm for the calculation of isoprene production. Experimental measurements of isoprene emission rates are expensive, however, and existing data are scarce and fragmentary. To overcome these difficulties, it is promising to develop a numerical model capable of precisely calculating the isoprene emission by trees for diverse ecosystems, even under changing environmental conditions. A basic process‐based biochemical isoprene emission model (BIM) has therefore been developed, which describes the enzymatic reactions in leaf chloroplasts leading to the formation of isoprene under varying environmental conditions (e.g. light intensity, temperature). Concentrations of the precursors of isoprene formation, 3‐phosphoglyceric acid and glyceraldehyde 3‐phosphate, are provided by a published light fleck photosynthesis model. Specific leaf and enzyme parameters were determined for the pedunculate oak (Quercus robur L.), so that the BIM is capable of calculating oak‐specific isoprene emission rates as influenced by the leaf temperature and light intensity. High correlation was observed between isoprene emission rates calculated by the BIM and the diurnal isoprene emission rates of leaves measured under controlled environmental conditions. The BIM was even capable of describing changes in isoprene emission caused by midday depression of net photosynthesis.     

The lipid transfer proteins (LTP) essentially concentrate in the skin of Rosaceae fruits as cell surface exposed allergens.

The localization and distribution of non-specific lipid transfer proteins (nsLTP) allergens in the skin and pulp of Rosaceae fruits (apple, peach, apricot, plum) has been investigated. nsLTP essentially concentrate in the pericarp of the fruits whereas the pulp contains lower amounts of allergens. Immunolocalization showed they are primarily located in the cytosol but are subsequently excreted and finally accumulate at the plasmalemma-cell wall interface and in the cell wall. However, high discrepancies were observed in the content of allergens among, e.g. different cultivars of apple. As a consequence, the consumption of peeled-off fruits is recommended to reduce the risk of severe allergic reactions (anaphylactic shock) in individuals sensitized to Rosaceae fruits.