Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions

Methods for site-specific modification of proteins should be quantitative and versatile with respect to the nature and size of the biological or chemical targets involved. They should require minimal modification of the target, and the underlying reactions should be completed in a reasonable amount of time under physiological conditions. Sortase-mediated transpeptidation reactions meet these criteria and are compatible with other labeling methods. Here we describe the expression and purification conditions for two sortase A enzymes that have different recognition sequences. We also provide a protocol that allows the functionalization of any given protein at its C terminus, or, for select proteins, at an internal site. The target protein is engineered with a sortase-recognition motif (LPXTG) at the place where modification is desired. Upon recognition, sortase cleaves the protein between the threonine and glycine residues, facilitating the attachment of an exogenously added oligoglycine peptide modified with the functional group of choice (e.g., fluorophore, biotin, protein or lipid). Expression and purification of sortase takes ∼3 d, and sortase-mediated reactions take only a few minutes, but reaction times can be extended to increase yields.National Institutes of Health (U.S.) (Grant RO1 AI08787

Site-Specific Chemoenzymatic Labeling of Aerolysin Enables the Identification of New Aerolysin Receptors

Aerolysin is a secreted bacterial toxin that perforates the plasma membrane of a target cell with lethal consequences. Previously explored native and epitope-tagged forms of the toxin do not allow site-specific modification of the mature toxin with a probe of choice. We explore sortase-mediated transpeptidation reactions (sortagging) to install fluorophores and biotin at three distinct sites in aerolysin, without impairing binding of the toxin to the cell membrane and with minimal impact on toxicity. Using a version of aerolysin labeled with different fluorophores at two distinct sites we followed the fate of the C-terminal peptide independently from the N-terminal part of the toxin, and show its loss in the course of intoxication. Making use of the biotinylated version of aerolysin, we identify mesothelin, urokinase plasminogen activator surface receptor (uPAR, CD87), glypican-1, and CD59 glycoprotein as aerolysin receptors, all predicted or known to be modified with a glycosylphosphatidylinositol anchor. The sortase-mediated reactions reported here can be readily extended to other pore forming proteins.National Institutes of Health (U.S.) (grant R01 AI087879

Un enfoque fisiológico para los procesos oceánicos y los cambios glaciares-interglaciares del CO2 atmosférico

18 pages, 6 figures, 1 table[EN] One possible path for exploring the Earth’s far-from-equilibrium homeostasis is to assume that it results from the organisation of optimal pulsating systems, analogous to that in complex living beings. Under this premise it becomes natural to examine the Earth’s organisation using physiological-like variables. Here we identify some of these main variables for the ocean’s circulatory system: pump rate, stroke volume, carbon and nutrient arterial-venous differences, inorganic nutrients and carbon supply, and metabolic rate. The stroke volume is proportional to the water transported into the thermocline and deep oceans, and the arterial-venous differences occur between recently-upwelled deep waters and very productive high-latitudes waters, with atmospheric CO2 being an indicator of the arterial-venous inorganic carbon difference. The metabolic rate is the internal-energy flux (here expressed as flux of inorganic carbon in the upper ocean) required by the system’s machinery, i.e. community respiration. We propose that the pump rate is set externally by the annual cycle, at one beat per year per hemisphere, and that the autotrophic ocean adjusts its stroke volume and arterial-venous differences to modify the internal-energy demand, triggered by long-period astronomical insolation cycles (external-energy supply). With this perspective we may conceive that the Earth’s interglacial-glacial cycle responds to an internal organisation analogous to that occurring in living beings during an exercise-recovery cycle. We use an idealised double-state metabolic model of the upper ocean (with the inorganic carbon/nutrients supply specified through the overturning rate and the steady-state inorganic carbon/nutrients concentrations) to obtain the temporal evolution of its inorganic carbon concentration, which mimics the glacial-interglacial atmospheric CO2 pattern[ES] Un posible camino para el estudio de la homeóstasis fuera-de-equilibrio de la tierra es suponer que resulta de la organización de sistemas pulsátiles optimizados, análoga a aquélla en seres vivos complejos. Bajo esta premisa parece natural examinar la organización de la tierra utilizando variables de tipo fisiológico. Aquí identificamos algunas de las principales variables del sistema circulatorio oceánico: tasa de bombeo del corazón, volumen de latido, diferencias arteriovenosas de carbono y nutrientes, suministro de carbono y nutrientes inorgánicos, y tasa metabólica. El volumen de latido es proporcional al transporte de agua hacia la termoclina y océano profundo, y las diferencias arterio-venosas ocurren entre las aguas profundas recientemente afloradas y aquellas altamente productivas de altas latitudes, con el CO2 atmosférico siendo un indicador de la diferencia arterio-venosa de carbono inorgánico. La tasa metabólica es el flujo de energía interna (aquí expresado como flujo de carbono inorgánico en el océano superior) requerido por la maquinaria que sostiene el sistema, i.e. respiración total de la comunidad. Se propone que la tasa de latido está impuesta externamente, un latido por año por hemisferio, y que el océano autotrófico ajusta su volumen de latido y las diferencias arteriovenosas a cambios en la demanda de energía interna, inducido por ciclos de insolación astronómica de largo período (suministro de energía externa). Bajo esta perspectiva podemos concebir que el ciclo interglacial-glacial de la tierra responde a una organización interna análoga a la que ocurre en seres vivos durante un ciclo de ejercicio-recuperación. Se utiliza un modelo metabólico idealizado de dos estados para el océano superior (con el suministro de carbono/nutrientes inorgánicos especificado mediante la tasa de recirculación de aguas profundas y las concentraciones de carbono/nutrientes inorgánicos en estado estacionario) para obtener la evolución temporal de su concentración de carbono inorgánico, la cual mimetiza el patrón glacial-interglacial del CO2 atmosféricoThis work was supported by the Spanish government through the CANOA project (CTM2005-00444/MAR)Peer reviewe

Site-specific protein modification using immobilized sortase in batch and continuous-flow systems

Transpeptidation catalyzed by ​sortase A allows the preparation of proteins that are site-specifically and homogeneously modified with a wide variety of functional groups, such as fluorophores, PEG moieties, lipids, glycans, bio-orthogonal reactive groups and affinity handles. This protocol describes immobilization of ​sortase A on a solid support (Sepharose beads). Immobilization of ​sortase A simplifies downstream purification of a protein of interest after labeling of its N or C terminus. Smaller batch and larger-scale continuous-flow reactions require only a limited amount of enzyme. The immobilized enzyme can be reused for multiple cycles of protein modification reactions. The described protocol also works with a Ca²⁺-independent variant of ​sortase A with increased catalytic activity. This heptamutant variant of ​sortase A (7M) was generated by combining previously published mutations, and this immobilized enzyme can be used for the modification of calcium-senstive substrates or in instances in which low temperatures are needed. Preparation of immobilized ​sortase A takes 1–2 d. Batch reactions take 3–12 h and flow reactions proceed at 0.5 ml h⁻¹, depending on the geometry of the reactor used.United States. National Institutes of Health (RO1 AI087879

Stochastic motion of test particle implies that G varies with time

The aim of this letter is to propose a new description to the time varying gravitational constant problem, which naturally implements the Dirac's large numbers hypothesis in a new proposed holographic scenario for the origin of gravity as an entropic force. We survey the effect of the Stochastic motion of the test particle in Verlinde's scenario for gravity\cite{Verlinde}. Firstly we show that we must get the equipartition values for $t\rightarrow\infty$ which leads to the usual Newtonian gravitational constant. Secondly,the stochastic (Brownian) essence of the motion of the test particle, modifies the Newton's 2'nd law. The direct result is that the Newtonian constant has been time dependence in resemblance as \cite{Running}.Comment: Accepted in International Journal of Theoretical Physic

The potential of marginal coastal nursery habitats for the conservation of a culturally important Caribbean marine species

Aim: Identifying the potential of marginal habitats for species conservation is of key importance when their core high-quality habitats are under substantial disturbances and threats. However, there is currently a knowledge gap on how useful marine marginal habitats may be for conserving endangered marine species. Here, we investigate the potential of groundwater-fed coastal areas for the conservation of the queen conch, an economically and culturally important marine gastropod. Location: The inlet of Xel-Ha, typical of groundwater-fed coastal areas widely distributed along the Yucatan Peninsula coast in Mexico and partially protected by a network of marine protected areas. Methods: We tracked 66 queen conchs (Lobatus gigas) using acoustic telemetry over a period of 3.5 years. We investigated for ontogenetic niche shift using a network analysis and by modelling their growth. Results: The queen conchs exhibited the same ontogenetic niche shift required to complete their life cycle in this marginal habitat as they do in offshore core habitats. A total of 33 individuals departed the inlet and migrated from shallow groundwater-affected nursery grounds to deeper marine habitats more suitable for breeding aggregation. Main conclusions: As the broad-scale movement behaviour of queen conch in this inlet is similar to that observed on the overfished core habitats, our findings suggest that groundwater-fed coastal areas should be included in conservation planning for an effective management of this species within a network of marine protected areas

In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation

In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington’s disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find tha