Evidence for Network Evolution in an Arabidopsis Interactome Map

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops

Variability and Action Mechanism of a Family of Anticomplement Proteins in Ixodes ricinus

Background: Ticks are blood feeding arachnids that characteristically take a long blood meal. They must therefore counteract host defence mechanisms such as hemostasis, inflammation and the immune response. This is achieved by expressing batteries of salivary proteins coded by multigene families. Methodology/Principal Findings: We report the in-depth analysis of a tick multigene family and describe five new anticomplement proteins in ixodes ricinus. Compared to previously described Ixodes anticomplement proteins, these segregated into a new phylogenetic group or subfamily. These proteins have a novel action mechanism as they specifically bind to properdin, leading to the inhibition of C3 convertase and the alternative complement pathway. An excess of non-synonymous over synonymous changes indicated that coding sequences had undergone diversifying selection. Diversification was not associated with structural, biochemical o, functional diversity, adaptation to host species or stage specificity but rather to differences in antigenicity. Conclusion/Significance: Anticomplement proteins from I. ricinus are the first inhibitors that specifically target a positive regulator of complement, properdin. They may provide new tools for the investigation of role of properdin in physiological and pathophysiological mechanisms. They may also be useful in disorders affecting the alternative complement pathway, Looking for and detecting the different selection pressures involved will help in understanding the evolution of multigene families and hematophagy in arthropods. © 2008 Couveur et al.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach

“De Novo” Design of Peptides with Specific Lipid-Binding Properties

In this study, we describe an in silico method to design peptides that can be made of non-natural amino acids and elicit specific membrane-interacting properties. The originality of the method holds in the capacities developed to design peptides from any non-natural amino acids as easily as from natural ones, and to test the structure stability by an angular dynamics rather than the currently-used molecular dynamics. The goal of this study was to design a non-natural tilted peptide. Tilted peptides are short protein fragments able to destabilize lipid membranes and characterized by an asymmetric distribution of hydrophobic residues along their helix structure axis. The method is based on the random generation of peptides and their selection on three main criteria: mean hydrophobicity and the presence of at least one polar residue; tilted insertion at the level of the acyl chains of lipids of a membrane; and conformational stability in that hydrophobic phase. From 10,000,000 randomly-generated peptides, four met all the criteria. One was synthesized and tested for its lipid-destabilizing properties. Biophysical assays showed that the “de novo” peptide made of non-natural amino acids is helical either in solution or into lipids as tested by Fourier transform infrared spectroscopy and is able to induce liposome fusion. These results are in agreement with the calculations and validate the theoretical approach

A single cell transcriptomic and proteomic map of the human liver

Introduction: The human liver is a complex organ composed of highly specialized parenchymal and non-parenchymal cells assembled in collaborative sinusoidal units within an extracellular matrix (ECM) network. Recent advances in ‘omics’ technologies allow the study of the whole transcriptome at single cell resolution, as well as the ECM composition of a whole organ. In this study, we aimed at providing a high-resolution transcriptomic and ECM proteomic map of the adult human liver. Methods: 80,000 liver cells from 2 human livers (Hepatic Biobank, Cliniques universitaires Saint-Luc) were loaded in a 10X Genomics instrument to generate 8 independent libraries, sequenced with the Illumina technology for an average of 65,000 reads per cells. Human liver fragments from 4 donors were decellularized by a combination of thermic and osmotic shocks, enzymatic digestion and use of detergents. Peptidic and proteomic composition of the resulting ECM was determined by LC/MS. Results: Distinct parenchymal and non-parenchymal cell populations and subpopulations were identified. Based on the expression of known metabolic markers, hepatocytes have been efficiently zonated along the portal-central axis, whereas newly identified, non-metabolic markers are currently evaluated for the zonation of non-parenchymal cells. Proteomic and peptidomic analysis reveals abundance of elastin and type I, II and VI collagens. Conclusions: Our study provides a unique dataset that paves the way for a thorough analysis of the microenvironment of human liver cells, and could prove to be of interest to liver stem cells researchers

Single cell RNA sequencing of the native human liver and its spatial resolution reveal new subpopulations of non-parenchymal cells.

Background: The liver’s multitude of vital functions are tightly linked to its complex assembly of highly specialized parenchymal and non-parenchymal cells in collaborative sinusoidal units. In the present study we aimed at providing the first high-resolution transcriptomic map of the infant and adult human liver by single-cell RNA sequencing, as a reference to understanding liver physiology and disease. Method: ~80,000 liver cells obtained after collagenase digestion of two human livers were loaded in a 10X Genomics instrument and sequenced using the Illumina technology to an average of 65,000 reads/cells. Results: A total of ~28,000 single-cell transcriptomes were generated, of which ~78%, 3% and 18% corresponds to hepatocytes, cholangiocytes and non-parenchymal cells, respectively. Taking specific gene expression patterns related to zonated liver functions (i.e. glutamine metabolism, urea cycle, bile acid synthesis, xenobiotic metabolism and albumine production) as a reference, the single-cell transcriptomes obtained for hepatocytes have efficiently been organized along the porto-central axis, revealing the pericentral-, periportal- and midzonal-specific hepatocyte transcriptomes. Within the clusters of cholangiocytes and non-parenchymal cells, our results identify multiple subpopulations, including two distinct populations of hepatic stellate cells, of which the transcriptomic disparities hint to intriguing functional subspecializations, and in situ hybridization suggests their spatial zonation in the liver lobule. Conclusion: Our study provides a transcriptomic atlas of the human native liver at an unparalleled resolution and contributes to a better understanding of the heterogeneity of the cellular compartments that underlies the physiology of the human liver

Study of Thermomyces lanuginosa Lipase in the Presence of Tributyrylglycerol and Water

The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze both hydrolysis at high water contents and transesterification in quasi-anhydrous conditions. Here, we investigated the Thermomyces lanuginosa lipase structure in solution in the presence of a tributyrin aggregate using 30 ns molecular-dynamics simulations. The water content of the active-site groove was modified between the runs to focus on the protein-water molecule interactions and their implications for protein structure and protein-lipid interactions. The simulations confirmed the high plasticity of the lid fragment and showed that lipid molecules also bind to a secondary pocket beside the lid. Together, these results strongly suggest that the lid plays a role in the anchoring of the protein to the aggregate. The simulations also revealed the existence of a polar channel that connects the active-site groove to the outside solvent. At the inner extremity of this channel, a tyrosine makes hydrogen bonds with residues interacting with the catalytic triad. This system could function as a pipe (polar channel) controlled by a valve (the tyrosine) that could regulate the water content of the active site