PIN-G – A novel reporter for imaging and defining the effects of trafficking signals in membrane proteins

Background  

The identification of protein trafficking signals, and their interacting mechanisms, is a fundamental objective of modern biology. Unfortunately, the analysis of trafficking signals is complicated by their topography, hierarchical nature and regulation. Powerful strategies to test candidate motifs include their ability to direct simpler reporter proteins, to which they are fused, to the appropriate cellular compartment. However, present reporters are limited by their endogenous expression, paucity of cloning sites, and difficult detection in live cells.     

Tag–probe labeling methods for live-cell imaging of membrane proteins

Instead of using reconstituted proteoliposomes, in situ investigations of membrane proteins in living cell membranes are important because the heterogeneous and dynamic nature of biomembranes significantly affects their behavior. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence measurements, particularly fluorescence microscopy. However, conventional genetic fusion with fluorescent proteins has several shortcomings. Post-translational labeling methods using a genetically encodable tag and synthetic probes targeting to the tag can overcome these limitations. This review summarizes emerging tag–probe techniques for labeling specific membrane proteins and their applications, including endocytotic internalization, partitioning to specific membrane domains, interprotein interactions, and conformational changes.     

Bifunctional selection–reporter systems for genetic transformation of citrus: mannose- and kanamycin-based systems

Agrobacterium-mediated transformation of Carrizo citrange [Citrus sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf.] with a binary vector containing a novel bifunctional reporter–selection fusion gene comprising an in-frame fusion between the manA gene and egfp gene is detailed. This system combined the phosphomannose isomerase positive selection system with the ability to monitor gene expression in a non-destructive manner using EGFP. Transgenic plants stably expressing the EGFP protein were regenerated following Agrobacterium-mediated transformation using a vector containing this fusion gene. We also obtained comparable transformation efficiencies when Carrizo explants were transformed using another Agrobacterium strain containing a binary vector with a bifunctional egfp–nptII fusion gene. Regenerating shoots were selected on medium containing 15 g L⁻¹ mannose supplemented with 5 g L⁻¹ sucrose for the manA-based selection or on medium containing 100 mg L⁻¹ kanamycin for the nptII-based selection. Our results indicated that the mannose-based antibiotic-free selection combined with visual identification of transgenic shoots using EGFP allows for early elimination of escape non-transgenic shoots and can provide a viable alternative to antibiotic-based selection systems in the genetic transformation of citrus and other crops.     

Are Rapid Immunoassays for in vivo Detection of Toxin A Sufficient for Diagnostic Purposes of Clostridium difficile -Associated Diseases?

One hundred and fifty-five stool specimens of patients suspected for Clostridium difficile -associated diarrhoea, colitis or pseudomembranous colitis (PMC) were investigated. All patients were pre-treated with antibiotics, suffered from watery diarrhoea and abdominal pain and were hospitalized in different hospital units. Units varied from departments of surgery, internal medicine, intensive care, paediatry, dermatology, orthopaedy to gastroenterology. Fifty C. difficile strains were isolated from the faecal samples. Clostridium difficile toxin detection was done directly in the stool samples, and also in cultured C. difficile strains (in vivo and in vitro, respectively). We observed clear differences between in vivo and in vitro toxin A detection by using commercial rapid immuno-enzymatic tests: from 25 in vivo toxin A-negative samples, 17 were positive in vitro. This observation suggests that culturing of C. difficile on selective medium is mandatory for adequate toxin detection and necessary for confirming the presence of toxin-producing C. difficile. This is especially important among patients with clinical symptoms and history of pretreatment with antibiotics and when in vivo toxin A detection is negative. It was established that toxin gene detection by PCR is optimal and PCR results were concordant with results of other in vitro assays. Genotyping by using AP-PCR and PCR ribotyping showed heterogeneity among the toxigenic C. difficile strains cultured from in vivo toxin A-negative stool samples.     

A circularly permuted β-lactamase as a novel reporter for evaluation of protein cyclization efficiency

Split inteins have been used as a versatile tool in protein engineering to mediate efficient in vivo and in vitro trans-splicing of a protein. The trans-splicing ability of split inteins was also applied to the in vivo cyclization of a protein. However, cyclization efficiency is dependent upon the type of split inteins employed and the conditions under which cyclization occur. In this study, a novel reporter system that easily measures the cyclization efficiency of split inteins was developed. For this purpose TEM-1 beta-lactamase was divided into two fragments (24 approximately 215 and 216 approximately 286 amino acids) and circularly permuted. The circularly permuted beta-lactamase expressed in Escherichia coli showed little beta-lactamase activity, most likely due to the structural modification of the protein. However, when the circularly permuted beta-lactamase was cyclized by the Synechocystis sp. PCC6803 DnaB split mini-intein, beta-lactamase activity both in vitro and in vivo was recovered. These results suggest that the novel reporter system can be exploited to develop new inteins with high efficiency of in vivo protein cyclization.     

A new setup for in vivo fluorescence imaging of photosynthetic activity

Here, we describe a new imaging setup able to assess in vivo photosynthetic activity. The system specifically measures time-resolved chlorophyll fluorescence in response to light. It is composed of a fast digital camera equipped with a wide-angle lens for the analysis of samples up to 10 × 10 cm, i.e. entire plants or petri dishes. In the choice of CCD, we have opted for a 12-bits high frame rate [150 fps (frames per second)] at the expense of definition (640 × 480 pixels). Although the choice of digital camera is always a compromise between these two related features, we have designed a flexible system allowing the fast sampling of images (down to 100 μs) with a maximum spatial resolution. This image readout system, synchronized with actinic light and saturating pulses, allows a precise determination of F ₀ and F _M, which is required to monitor PSII activity. This new imaging system, together with image processing techniques, is useful to investigate the heterogeneity of photosynthetic activity within leaves or to screen large numbers of unicellular algal mutant colonies to identify those with subtle changes in photosynthetic electron flow.     

Preparation of reconstituted acetylcholine receptor membranes suitable for AFM imaging of lipid–protein interactions

The nicotinic acetylcholine receptor (nAChR) has been reconstituted in POPC vesicles at high lipid–protein (L/P) ratios for the preparation of supported lipid bilayers with a low protein density for studies of protein–lipid interactions using atomic force microscopy (AFM). Initial reconstitutions using a standard dialysis method with bulk L/P ratios ranging from 20:1 to 100:1 (w/w) gave heterogeneous samples that contained both empty vesicles and proteoliposomes with a range of L/P ratios. This is problematic because empty vesicles adsorb and rupture to form bilayer patches more rapidly than do protein-rich vesicles, resulting in the loss of protein during sample washing. Although it was not possible to find reconstitution conditions that gave homogeneous populations of vesicles with high L/P ratios, an additional freeze–thaw cycle immediately after dialysis did reproducibly yield a fraction of proteoliposomes with L/P ratios above 100:1. These proteoliposomes were separated by sucrose gradient centrifugation and used to prepare supported bilayers with well-separated individual receptors and minimal adsorbed proteoliposomes. AFM images of such samples showed many small features protruding from the bilayer surface. These features range in height from 1 to 5 nm, consistent with the smaller intracellular domain of the protein exposed, and have lateral dimensions consistent with an individual receptor. Some bilayers with reconstituted protein also had a small fraction of higher features that are assigned to nAChR with the larger extracellular domain exposed and showed evidence for aggregation to give dimers or small oligomers. This work demonstrates the importance of using highly purified reconstituted membranes with uniform lipid–protein ratios for AFM studies of integral membrane protein–lipid interactions.     

A micropatterning approach for imaging dynamic Cx43 trafficking to cell–cell borders

The precise expression and timely delivery of connexin 43 (Cx43) proteins to form gap junctions are essential for electrical coupling of cardiomyocytes. Growing evidence supports a cytoskeletal-based trafficking paradigm for Cx43 delivery directly to adherens junctions at the intercalated disc. A limitation of Cx43 localization assays in cultured cells, in which cell–cell contacts are essential, is the inability to control for cell geometry or reproducibly generate contact points. Here we present a micropatterned cell pairing system well suited for live microscopy to examine how the microtubule and actin cytoskeleton confer specificity to Cx43 trafficking to precisely defined cell–cell junctions. This system can be adapted for other cell types and used to study dynamic intracellular movements of other proteins important for cell–cell communication.     

Toxin–antitoxin systems: why so many,what for?

Toxin-antitoxin (TA) systems are small genetic modules that are abundant in bacterial genomes. Three types have been described so far, depending on the nature and mode of action of the antitoxin component. While type II systems are surprisingly highly represented because of their capacity to move by horizontal gene transfer, type I systems appear to have evolved by gene duplication and are more constrained. Type III is represented by a unique example located on a plasmid. Type II systems promote stability of mobile genetic elements and might act at the selfish level. Conflicting hypotheses about chromosomally encoded systems, from programmed cell death and starvation-induced stasis to protection against invading DNA and stabilization of large genomic fragments have been proposed.     

A New 5′-Protecting Group for Use in Solid-Phase Synthesis of Oligoribonucleotides

Abstract

The 2-(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl (DNBSB) group is proposed as a protecting group for the 5′-position of nucleosides. The DNBSB group may be removed under mild non-acidic conditions and may have potential in solid-phase synthesis of oligoribo- and oligodeoxyribonucleotides.     

Structure–activity relationship of lipid core peptide-based Group A Streptococcus vaccine candidates

Infection with Group A Streptococcus (GAS) can result in a range of different illnesses, some of which are fatal. Currently, our efforts to develop a vaccine against GAS focuses on the lipid core peptide (LCP) system, a subunit vaccine containing a lipoamino acid (LAA) moiety which allows the stimulation of systemic antibody activity. In the present study, a peptide (J14) representing the B-cell epitope from the GAS M protein was incorporated alongside a universal T-helper epitope (P25) in four LCP constructs of different spatial orientation or LAA lengths. Through structure–activity studies, it was discovered that while the alteration of the LCP orientation had a weaker effect on immunostimulation, increasing the LAA side chain length within the construct increased antibody responses in murine models. Furthermore, the mice immunised with the lead LCP construct were also able to maintain antibody activity throughout the course of five months. These findings highlight the importance of LAA moieties in the development of intranasal peptide vaccines and confirmed that its side chain length has an effect on the immunogenicity of the structure.     

Synthesis and biological evaluation of 11C-labeled β-galactosyl triazoles as potential PET tracers for in vivo LacZ reporter gene imaging

In our aim to develop LacZ reporter probes with a good retention in LacZ expressing cells, we report the synthesis and preliminary evaluation of two carbon-11 labeled β-galactosyl triazoles 1-(β-d-galactopyranosyl)-4-(p-[¹¹C]methoxyphenyl)-1,2,3-triazole ([¹¹C]-6) and 1-(β-d-galactopyranosyl)-4-(6-[¹¹C]methoxynaphthyl)-1,2,3-triazole ([¹¹C]-13). The precursors for the radiolabeling and the non-radioactive analogues (6 and 13) were synthesized using straightforward ‘click’ chemistry. In vitro incubation experiments of 6 with β-galactosidase in the presence of o-nitrophenyl β-d-galactopyranoside (ONPG) showed that the triazolic compound was an inhibitor of β-galactosidase activity. Radiolabeling of both precursors was performed using [¹¹C]methyl iodide as alkylating agent at 70 °C in DMF in the presence of a small amount of base. The log P values were ?0.1 and 1.4, respectively, for [¹¹C]-6 and [¹¹C]-13, the latter therefore being a good candidate for increased cellular uptake via passive diffusion. Biodistribution studies in normal mice showed a good clearance from blood for both tracers. [¹¹C]-6 was mainly cleared via the renal pathway, while the more lipophilic [¹¹C]-13 was excreted almost exclusively via the hepatobiliary system. Despite the lipophilicity of [¹¹C]-13, no brain uptake was observed. Reversed phase HPLC analysis of murine plasma and urine revealed high in vivo stability for both tracers. In vitro evaluation in HEK-293T cells showed an increased cell uptake for the more lipophilic [¹¹C]-13, however, there was no statistically higher uptake in LacZ expressing cells compared to control cells.     

A rapid method for liquid β-galactosidase reporter assay in Saccharomyces cerevisiae

Although β-galactosidase assay is widely used for various studies in yeast a quantitative estimation of low enzyme activities with standard reactives remains hampered. It requires long reaction time and large amounts of cells. To overcome existing limitations we developed protocol, which incorporates realization reaction in miniaturized format, cell lysis in reaction buffer and simplification the normalization of β-galactosidase activity. These features allow faster reaction kinetics, accurate and simple quantification of low enzyme activities. To perform studies in vivo conditions we constructed a reporter plasmids based on the low copy yeast vector Ycp50. We adapted our assay on the yeast protein Rpn4 which is highly unstable with a half-life of only 2 min. We demonstrated that detection of Rpn4–LacZ fusion is achieved in 40 min in our method, whereas in standard assay it requires 4–5 h. Moreover, we implemented our approach for promoter dissection investigation. Thus, we present rapid, convenient and less labor-intensive method for assessment β-galactosidase activity.     

In Silico Derived Peptides for Inhibiting the Toxin–Antitoxin Systems of Mycobacterium tuberculosis: Basis for Developing Peptide-Based Therapeutics

Toxin–antitoxin (TA) systems of Mycobacterium tuberculosis (Mtb) is a prerequisite for the bacterium to survive in extreme conditions. Antimicrobial peptides inhibiting the formation of these complexes provide a novel strategy for TB drug discovery process. Absence of TA genes in human, makes these systems as an attractive target for drug development. In this study using Peptiderive server, we have derived a number of potential inhibitory peptides for nine TA complexes—VapBC3, VapBC5, VapBC11, VapBC15, VapBC26, VapBC30, RelBE2, RelJK, MazEF4 of Mtb. We have studied about the common interacting toxin residues with the antitoxin and with the derived peptide. Further, using Cluspro server, we compared the binding efficacy of the in silico derived peptides with the published potential peptides for the toxins VapC26, VapC30 and MazF. Thus, these in silico derived peptides would serve as basis for developing peptide based therapeutics for TA complexes of Mtb.

     

Zoo Playgrounds: A Source of Enrichment or Stress for a Group of Nearby Cockatoos? A Case Study

There is increasing evidence that in some circumstances, zoo visitors may be aversive stimuli to nonhuman animals housed in zoos. Yet, most previous research has focused on primates with little attention given to numerous other species who are housed in zoos. The focus animal of this project was the cockatoo, a species who has received minimal attention in zoo-based research. Furthermore, although the influence of the zoo setting has become increasingly important in visitor effect studies, this is the 1st study to quantify the effect of activity at a children's playground on zoo animals. There was an investigation on the effect of a zoo playground on the behavior of citron-crested and Moluccan cockatoos (Cacatua sulphurea citrinocristata and Cacatua moluccensis), as well as the effect of children standing in front of the birds' aviaries. The results showed that in some circumstances, the Moluccan cockatoos retreated from visitors, while the citron-crested cockatoos did not retreat from visitors and became more social in the presence of visitors. These findings highlight the importance of careful selection of species and individual animals to be housed near zoo playgrounds.     

Fluorogenic ‘click-on’ dendrimer reporter for rapid profiling of cell proliferation

The application of small molecule fluorescent reporters to monitor biological systems is limited by their poor water solubility and background fluorescence of these reporters. Herein, we describe the synthesis and testing of a fluorogenic ‘click’ dendrimer reporter to monitor cellular processes. The reporter system consists of a polyamidoamine (PAMAM) dendrimer conjugated with 3-azido-7-hydroxy coumarin. After the copper(I)-catalyzed azide–alkyne cycloaddition reaction (‘click’ reaction) with alkyne-derivatized target molecules, the natively non-fluorescent construct has a strong enhancement in fluorescence. This fluorogenic dendrimer reporter can be used to efficiently monitor biological processes and the specificity afforded by the ‘click’ reaction greatly reduces background noise and enhances assay flexibility. We used this fluorogenic dendrimer reporter to monitor incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into newly synthesized DNA, as a surrogate marker of cellular proliferation. We anticipate that this new class of fluorogenic reporter can be used to monitor a wide array of molecules and lends itself to high-throughput profiling of biological systems.     

Chlorophyll fluorescence imaging of plant–pathogen interactions

Chlorophyll fluorescence imaging provides a noninvasive, non-destructive method with which to measure heterogenous changes in photosynthetic metabolism in plants infected by pathogens. The availability of commercial imaging fluorimeters has helped make this technique available to the wider scientific community, but considerable care is needed, both in experimental design and in the interpretation of results, to make the most of this powerful analytical tool. The origins of changes in chlorophyll fluorescence yield are discussed and the use of conventional and novel combinatorial imaging approaches explored, together with complementary techniques such as thermal imaging. This review examines the use of chlorophyll fluorescence imaging as a method for the early detection of viral, bacterial and fungal infection, before symptoms are visible by eye, and also as a means with which to probe underlying pathogen-induced changes in host physiology in both compatible and incompatible interactions. The use of chlorophyll fluorescence imaging to study host physiology is greatly enhanced when the atmosphere around the leaf is manipulated and simultaneous measurements of gas exchange made: The cost to the host plant of different resistance mechanisms can be calculated, the fate of the products of photosynthetic electron transport determined and localised alterations in the source–sink status of host tissue visualised.