Omnipresent Maxwell’s demons orchestrate information management in living cells

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the informationmanaging agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell’s demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers

El cuento para desarrollar procesos matemáticos

Esta experiencia promueve el establecimiento de conexiones para la construcción de conocimiento en el aula de primaria. Las actividades se diseñan a partir de la lectura y la comprensión del cuento El reino de la geometría a fin de desarrollar procesos matemáticos de manera conectada con el desarrollo de competencias artísticas y lingüísticas

Proteolytic Processing of Nlrp1b Is Required for Inflammasome Activity

Nlrp1b is a NOD-like receptor that detects the catalytic activity of anthrax lethal toxin and subsequently co-oligomerizes into a pro-caspase-1 activation platform known as an inflammasome. Nlrp1b has two domains that promote oligomerization: a NACHT domain, which is a member of the AAA+ ATPase family, and a poorly characterized Function to Find Domain (FIIND). Here we demonstrate that proteolytic processing within the FIIND generates N-terminal and C-terminal cleavage products of Nlrp1b that remain associated in both the auto-inhibited state and in the activated state after cells have been treated with lethal toxin. Functional significance of cleavage was suggested by the finding that mutations that block processing of Nlrp1b also prevent the ability of Nlrp1b to activate pro-caspase-1. By using an uncleaved mutant of Nlrp1b, we established the importance of cleavage by inserting a heterologous TEV protease site into the FIIND and demonstrating that TEV protease processed this site and induced inflammasome activity. Proteolysis of Nlrp1b was shown to be required for the assembly of a functional inflammasome: a mutation within the FIIND that abolished cleavage had no effect on self-association of a FIIND-CARD fragment, but did reduce the recruitment of pro-caspase-1. Our work indicates that a post-translational modification enables Nlrp1b to function

The stoichiometric interaction of the Hsp90-Sgt1-Rar1 complex by CD and SRCD spectroscopy

While the molecular details by which Hsp90 interacts with Sgt1 and Rar1 were previously described the exact stoichiometric complex that is formed remains elusive. Several possibilities remain that include two asymmetric complexes, Sgt12-Hsp902-Rar12 (two molecules of Sgt1 and Rar1 and one Hsp90 dimer) or Sgt12-Hsp902-Rar11 (with a single Rar1 molecule) and an asymmetric complex (Sgt11-Hsp902-Rar11). The Hsp90-mediated activation of NLR receptors (Nucleotide-binding domain and Leucine-rich Repeat) in the innate immunity of both plants and animals is dependent on the co-chaperone Sgt1 and in plants on Rar1, a cysteine- and histidine-rich domain (CHORD)-containing protein. The exact stoichiometry of such a complex may have a direct impact on NLR protein oligomerization and thus ultimately on the mechanism by which NLRs are activated. CD spectroscopy was successfully used to determine the stoichiometry of a ternary protein complex among Hsp90, Sgt1, and Rar1 in the presence of excess ADP. The results indicated that a symmetric Sgt12-Hsp902-Rar11 complex was formed that could allow two NLR molecules to simultaneously bind. The stoichiometry of this complex has implications on, and might promote, the dimerization of NLR proteins following their activation

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms

Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks across species is not trivial. The definition of a biologically meaningful module is not a fixed one and changing the distance threshold that defines the degree of coexpression gives rise to different modules. As a result when comparing modules across species, many different partially overlapping conserved module pairs across species exist and deciding which pair is most relevant is hard. Therefore, we developed a method referred to as conserved modules across organisms (COMODO) that uses an objective selection criterium to identify conserved expression modules between two species. The method uses as input microarray data and a gene homology map and provides as output pairs of conserved modules and searches for the pair of modules for which the number of sharing homologs is statistically most significant relative to the size of the linked modules. To demonstrate its principle, we applied COMODO to study coexpression conservation between the two well-studied bacteria Escherichia coli and Bacillus subtilis. COMODO is available at: http://homes.esat.kuleuven.be/∼kmarchal/Supplementary_Information_Zarrineh_2010/comodo/index.html

ABC transporter architecture and regulatory roles of accessory domains

AbstractWe present an overview of the architecture of ATP-binding cassette (ABC) transporters and dissect the systems in core and accessory domains. The ABC transporter core is formed by the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) that constitute the actual translocator. The accessory domains include the substrate-binding proteins, that function as high affinity receptors in ABC type uptake systems, and regulatory or catalytic domains that can be fused to either the TMDs or NBDs. The regulatory domains add unique functions to the transporters allowing the systems to act as channel conductance regulators, osmosensors/regulators, and assemble into macromolecular complexes with specific properties

The inducer maltotriose binds in the central cavity of the tetratricopeptide-like sensor domain of MalT, a bacterial STAND transcription factor

International audienceSignal transduction ATPases with numerous domains (STAND) are sophisticated proteins that integrate several signals and respond by building multimeric platforms allowing signaling in various processes: apoptosis, innate immunity, bacterial metabolism. They comprise a conserved nucleotide oligomerization domain (NOD), which functions as a binary switch that oscillates between the OFF (ADP-bound) and the ON (ATP-bound) conformation, and non conserved sensor and effector domains. Transition from the OFF form to the ON form strictly depends on the binding of an inducer to the sensor domain. The interaction of the inducer with this domain was studied in MalT, a model STAND protein. MalT sensor domain has a SUPR (superhelical repeats) fold resembling a cylinder with a central cavity. The cavity was subjected to an alanine-scanning approach, and the effects of the alanine substitutions on inducer binding and transcription activation were analyzed. This work unambiguously showed that the inducer maltotriose binds inside the cavity, and a patch on the inner surface was proposed to be the primary maltotriose binding-site. Furthermore, limited proteolysis suggested that maltotriose binding changes the conformation of the sensor domain

Solides à dimensionnalité réduite

The two-dimensional or one-dimensional character of a structure is related to an important anisotropy of the chemical bonds. Such solids can be considered as built up of layers or chains, the internal cohesion of which is due to strong iono-covalent or metallic bounds. On the contrary, interlayer or interchain bonds are weak, generally of the Van der Waals type. The existence of such independant structural units involves crystallographic, chemical and physical consequences : — the weakness of the interlayer or interchain bonds allows gliding motions which lead to polytypism, — this weakness also allows the slabs or chains to be pulled apart through various intercalations (alkali or alkaline earth metals, organic molecules, ammonia), — the structural anisotropy results in an important anisotropy of the physical properties. Fermi surfaces with large parallel portions can allow charge density waves to occur. These facts are illustrated with some examples chosen among transition metal chalcogenides : two dimensionality of the TX₂ dichalcogenides, pseudo-one-dimensionality of compounds such as NbSe₃ and I[x]NbSe₄.Le caractère bidimensionnel ou unidimensionnel d'une structure provient d'une très forte anisotropie des liaisons chimiques qui y sont mises en jeu. Un tel solide est construit à partir d'individualités structurales telles que feuillets ou fibres. A l'intérieur de ces entités, les liaisons sont fortes (ionocovalentes ou métalliques). Entre feuillets ou fibres les liaisons sont faibles, généralement de type Van der Waals. L'existence d'unités structurales nettement individualisées implique des conséquences cristallographiques, chimiques et physiques : — la faiblesse des liaisons qui s'exercent entre individualités structurales voisines en autorise le glissement relatif. Ceci explique la multiplicité des formes polytypiques observées par exemple pour les composés lamellaires, — cette faiblesse permet également d'écarter feuillets ou fibres par le jeu des diverses insertions envisageables (alcalins, alcalino-terreux, molécules organiques, ammoniac), — l'anisotropie géométrique de telles structures se traduit par ailleurs par une grande anisotropic des propriétés physiques. Enfin, l'existence de surfaces de Fermi à larges portions parallèles peut déterminer l'apparition d'ondes de densité de charge. Ces faits sont illustrés à l'aide d'exemples choisis parmi les chalcogénures d'éléments de transition : bidimensionnalité des dichalcogénures TX₂, pseudo-unidimensionnalité de composés tels que NbSe₃ et I[x]NbSe₄.Danot Michel. Solides à dimensionnalité réduite. In: Bulletin de Minéralogie, volume 103, 3-4, 1980. Propriétés des solides minéraux. I. Dissolution. II. Ordre-désordre