Delineation of critical amino acids in activation function 1 of progesterone receptor for recruitment of transcription coregulators

The activation functions AF1 and AF2 of nuclear receptors mediate the recruitment of coregulators in gene regulation. AF1 is mapped to the highly variable and intrinsically unstructured N terminal domain and AF2 lies in the conserved ligand binding domain. The unstructured nature of AF1 offers structural plasticity and hence functional versatility in gene regulation. However, little is known about the key functional residues of AF1 that mediates its interaction with coregulators. This study focuses on the progesterone receptor (PR) and reports the identification of K464, K481 and R492 (KKR) as the key functional residues of PR AF1. The KKR are monomethylated and function cooperatively. The combined mutations of KKR to QQQ render PR isoform B (PRB) hyperactive, whereas KKR to FFF mutations abolishes as much as 80% of PR activity. Furthermore, the hyperactive QQQ mutation rescues the loss of PR activity due to E911A mutation in AF2. The study also finds that the magnitudes of the mutational effect differ in different cell types as a result of differential effects on the functional interaction with coregulators. Furthermore, KKR provides the interface for AF1 to physically interact with p300 and SRC-1, and with AF2 at E911. Intriguingly, the inactive FFF mutant interacts strikingly stronger with both SRC-1 and AF2 than wt PRB. We propose a tripartite model to describe the dynamic interactions between AF1, AF2 and SRC-1 with KKR of AF1 and E911 of AF2 as the interface. An overly stable interaction would hamper the dynamics of disassembly of the receptor complex.     

Expression and membrane integration of SARS-CoV M protein

SARS-CoV M gene fragment was cloned and expressed as a recombinant protein fused with a V5 tag at the C-terminus in Vero E6 cells. In addition to un-glycosylated and glycosylated proteins, one product with smaller size initiated in-frame from the third Met residues probably through ribosomal re-initiation was also detected. Translation initiated in-frame from the third Met is unusual since the sequence around the first Met of SARS-CoV M protein contains the optimal consensus Kozak sequence. The function of this smaller translated product awaits further investigation. Similar to other N-glycosylated proteins, glycosylation of SARS-CoV M protein was occurred co-translationally in the presence of microsomes. The SARS-CoV M protein is predicted as a triple-spanning membrane protein lack of a conventional signal peptide. The second and third trans-membrane regions (a.a. 46–68 and 78–100) are predicted to be the primary type helices, which will be able to penetrate into membrane by themselves, while the first trans-membrane region (a.a. 14–36) is predicted to be the secondary type helix, which is considered to be stabilized by the interaction with other trans-membrane segments. As expected, the second and third trans-membrane regions were able to insert a cytoplasmic protein into the endoplasmic reticulum membrane more efficiently than the first one. These results should be important for the study of SARS-CoV morphogenesis. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Assembly and regulation of acetylcholinesterase at the vertebrate neuromuscular junction

The collagen-tailed form of acetylcholinesterase (ColQ-AChE) is the major if not unique form of the enzyme associated with the neuromuscular junction (NMJ). This enzyme form consists of catalytic and non-catalytic subunits encoded by separate genes, assembled as three enzymatic tetramers attached to the three-stranded collagen-like tail (ColQ). This synaptic form of the enzyme is tightly attached to the basal lamina associated with the glycosaminoglycan perlecan. Fasciculin-2 is a snake toxin that binds tightly to AChE. Localization of junctional AChE on frozen sections of muscle with fluorescent Fasciculin-2 shows that the labeled toxin dissociates with a half-life of about 36h. The fluorescent toxin can subsequently be taken up by the muscle fibers by endocytosis giving the appearance of enzyme recycling. Newly synthesized AChE molecules undergo a lengthy series of processing events before final transport to the cell surface and association with the synaptic basal lamina. Following co-translational glycosylation the catalytic subunit polypeptide chain interacts with several molecular chaperones, glycosidases and glycosyltransferases to produce a catalytically active enzyme that can subsequently bind to one of two non-catalytic subunits. These molecular chaperones can be rate limiting steps in the assembly process. Treatment of muscle cells with a synthetic peptide containing the PRAD attachment sequence and a KDEL retention signal results in a large increase in assembled and exportable AChE, providing an additional level of post-translational control. Finally, we have found that Pumilio2, a member of the PUF family of RNA-binding proteins, is highly concentrated at the vertebrate neuromuscular junction where it plays an important role in regulating AChE translation through binding to a highly conserved NANOS response element in the 3'-UTR. Together, these studies define several new levels of AChE regulation in electrically excitable cells.     

Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis

Brachypodium distachyon is a promising model system for the structural and functional genomics of temperate grasses because of its physical, genetic and genome attributes. The sequencing of the inbred line Bd21 ( http://www.brachypodium.org ) started in 2007. However, a transformation method remains to be developed for the community standard line Bd21. In this article, a facile, efficient and rapid transformation system for Bd21 is described using Agrobacterium -mediated transformation of compact embryogenic calli (CEC) derived from immature embryos. Key features of this system include: (i) the use of the green fluorescent protein (GFP) associated with hygromycin selection for rapid identification of transgenic calli and plants; (ii) the desiccation of CEC after inoculation with Agrobacterium ; (iii) the utilization of Bd21 plants regenerated from tissue culture as a source of immature embryos; (iv) the control of the duration of the selection process; and (v) the supplementation of culture media with CuSO₄ prior to and during the regeneration of transgenic plants. Approximately 17% of CEC produced transgenic plants, enabling the generation of hundreds of T-DNA insertion lines per experiment. GFP expression was observed in primary transformed Bd21 plants (T₀) and their progeny (T₁). The Mendelian inheritance of the transgenes was confirmed. An adaptor-anchor strategy was developed for efficient retrieval of flanking sequence tags (FSTs) of T-DNA inserts, and the resulting sequences are available in public databases. The production of T-DNA insertion lines and the retrieval of associated FSTs reported here for the reference inbred line Bd21 will facilitate large-scale functional genomics research in this model system.     

Temperature-assisted high hydrostatic pressure inactivation of Staphylococcus aureus in a ham model system: evaluation in selective and nonselective medium

Aims: The purpose of this study was to investigate the inactivation kinetics of Staphylococcus aureus in a ham model system by high hydrostatic pressure at ambient (25°C) and selected temperatures (45, 55°C). Selective [Baird Parker (BP) agar] and nonselective [brain heart infusion (BHI) agar] growth media were used for enumeration in order to count viable and sublethally injured cells. Methods and Results: The micro‐organism was exposed to a range of pressures (450, 500, 550, 600 MPa) at ambient temperature (25°C) for up to 45 min. Additionally, the behaviour of the micro‐organism was evaluated at mild temperatures in combination with high pressure treatment, namely: (i) 350, 400 and 450 MPa at 45°C; and (ii) 350 and 400 MPa at 55°C, for up to 12 min. Inactivation kinetics were calculated in terms of D_p and z_p values. Survival curves of S. aureus at ambient temperature were mostly linear, whereas when temperature was applied, tailing was observed in most survival curves. The estimated D_p values and therefore the number of surviving cells, were substantially higher on the selective BP agar in the whole range of pressures applied, indicating that S. aureus showed greater recovery in the selective BP agar than the nonselective BHI agar. Samples pressurized at ambient temperature needed higher pressures (over 500 MPa) to achieve a reduction of the population of the pathogen more than 5 log CFU ml^?1. The same level of inactivation was achieved at lower pressure levels when mild heating was simultaneously applied. Indeed, more than 6 log CFU ml^?1 reductions were obtained at 400 MPa and 55°C within the first 7 min of the process in BHI medium. Conclusion: Elevated temperatures allowed lower pressure levels and shorter processing times of pathogen inactivation than at room temperature. Greater recovery of the pathogen was observed in the selective (BP agar) medium, regardless of pressure and temperature applied. Significance and Impact of the Study: The obtained kinetics could be employed by the industry in selecting optimum pressure/temperature processing conditions. Attention must be given to the selection of the enumeration medium, as the use of an inappropriate medium would lead to underestimation of the surviving cells, thus imposing a risk in the microbiological safety of the product.     

Evaluation of the influence of anisotropic indirect nuclear spin-spin coupling tensors on effective residual dipolar couplings for model peptides

Residual dipolar couplings (RDCs) observed between nuclear spins in molecules in partially oriented media have become a valuable source of information for NMR spectroscopists seeking to structurally characterize biological macromolecules. Examination of the form of the direct (D) and indirect (J) nuclear spin-spin coupling Hamiltonians indicates that all observed RDCs contain an unknown contribution from the anisotropic part of J (J) in addition to the direct dipolar contribution, D _PQ. Here, we evaluate the influence of J on RDCs through a series of DFT calculations on model peptides. Very small corrections to one-bond RDCs measured between heavy atoms in peptides and proteins are recommended: +0.51% for N-C spin pairs, and +0.45% for C-C spin pairs. The corrections to RDCs involving at least one proton are negligible. This latter point is likely to be equally applicable to nucleic acids and oligosaccharides in addition to peptides and proteins. Finally, the orientations of the J(N, C) and J(C, C) tensors in the molecular framework are reported for glycylglycine.     

Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium meliloti in the alfalfa (Medicago sativa) rhizosphere

The colonization ability of Pseudomonas fluorescens F113rif in alfalfa rhizosphere and its interactions with the alfalfa microsymbiont Sinorhizobium meliloti EFB1 has been analyzed. Both strains efficiently colonize the alfalfa rhizosphere in gnotobiotic systems and soil microcosms. Colonization dynamics of F113rif on alfalfa were similar to other plant systems previously studied but it is displaced by S. meliloti EFB1, lowering its population by one order of magnitude in co-inoculation experiments. GFP tagged strains used to study the colonization patterns by both strains indicated that P. fluorescens F113rif did not colonize root hairs while S. meliloti EFB1 extensively colonized this niche. Inoculation of F113rif had a deleterious effect on plants grown in gnotobiotic systems, possibly because of the production of HCN and the high populations reached in these systems. This effect was reversed by co-inoculation. Pseudomonas fluorescens F113 derivatives with biocontrol and bioremediation abilities have been developed in recent years. The results obtained support the possibility of using this bacterium in conjunction with alfalfa for biocontrol or rhizoremediation technologies.