SNAP-tag technology optimized for use in Entamoeba histolytica

Hybrid labeling system for dSTORM imaging of endoplasmic reticulum for uncovering ultrastructural transformations under stress conditions

The endoplasmic reticulum (ER) transforms its morphology to fit versatile cellular functions especially under stress conditions. Since various ER stresses are critical pathophysiological factors, the precise observations of ER can provide insights into disease diagnoses and biological researches. Live-cell super-resolution imaging is highly expected for uncovering microstructures of ER. However, to achieve this, there remains a big challenge in how to efficiently label ER with advanced fluorophores. Herein, we report a new SNAP-tag fluorescent probe, namely, CLP-TMR, for specific and high-density labeling of the newly constructed dual ER-signal (targeting and retention) peptides fused-SNAP proteins. This hybrid labeling system integrating chemical probes with genetically encoded techniques enables molecular position reconstructions of ER morphologies through direct stochastic optical reconstruction microscopy (dSTORM) imaging. The super-resolution imaging reveals several never-known ultrastructural changes responding to different ER stresses, i.e. the formation of peripheral ER sheets to restore the immunogenicity, and the long flattened ER tubules under inflammation.

Dermal fibroblast cells interactions with single and triple bacterial-species biofilms

Polymicrobial biofilm leads to wound healing delay. We set up an in vitro co-culture model of single- and triple-species biofilms of Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecalis with dermal fibroblast to assess the fibroblast response against to the different biofilms. Scratch and viability assays and biofilm cell quantifications were performed by WST-1, CLSM and plating method, respectively. Quorum sensing-related gene expression levels in P. aeruginosa and E. faecalis were analysed by reverse-transcriptase PCR. The immune responses of cells against S. aureus, P. aeruginosa and E. faecalis biofilms were measured by cytokine and matrix metalloproteinase analyzes. The influence of biofilm soluble factors on fibroblasts was also determined. After 24 h, triple-species biofilm cells caused the removal of the fibroblasts from the surfaces indicating the negative synergistic effect of three species. After co-cultures, twenty-five cytokines were significantly increased in fibroblast cells compared to control. Compared to other strains, the most important cytokine, chemokine and growth factors increased was observed in P. aeruginosa co-cultures with fibroblast. While the expressions of fsrB and gelE genes were significantly upregulated in E. faecalis biofilm cells cultured with fibroblast cells, no significant difference was observed in P. aeruginosa. The wound healing and cell growth of fibroblasts were disrupted more aggressively in the presence of P. aeruginosa and triple-species biofilm cells. P. aeruginosa generally induced a stronger immune response in the fibroblasts than E. faecalis and S. aureus.

Red fluorescent protein (DsRFP) optimization for Entamoeba histolytica expression

Entamoeba histolytica genetic organization and genome structure is complex and under intense research. The genome is fully sequenced, and several tools have been developed for the molecular study of this organism. Nevertheless, good protein tracking tags that are easy to measure and image, like the fluorescent proteins are lacking. In this report, we codon-optimized the red fluorescent protein from the coral Discosoma striata (DsRFP) for its use in E. histolytica and demonstrated functionality in vivo. We envision that this protein can be widely used for the development of transcriptional reporter systems and protein-tagging applications.

Knockdown of Five Genes Encoding Uncharacterized Proteins Inhibits Entamoeba histolytica Phagocytosis of Dead Host Cells

Entamoeba histolytica is the protozoan parasite that causes invasive amebiasis, which is endemic to many developing countries and characterized by dysentery and liver abscesses. The virulence of E. histolytica correlates with the degree of host cell engulfment, or phagocytosis, and E. histolytica phagocytosis alters amebic gene expression in a feed-forward manner that results in an increased phagocytic ability. Here, we used a streamlined RNA interference screen to silence the expression of 15 genes whose expression was upregulated in phagocytic E. histolytica trophozoites to determine whether these genes actually function in the phagocytic process. When five of these genes were silenced, amebic strains with significant decreases in the ability to phagocytose apoptotic host cells were produced. Phagocytosis of live host cells, however, was largely unchanged, and the defects were surprisingly specific for phagocytosis. Two of the five encoded proteins, which we named E. histolytica ILWEQ (EhILWEQ) and E. histolytica BAR (EhBAR), were chosen for localization via SNAP tag labeling and localized to the site of partially formed phagosomes. Therefore, both EhILWEQ and EhBAR appear to contribute to E. histolytica virulence through their function in phagocytosis, and the large proportion (5/15 [33%]) of gene-silenced strains with a reduced ability to phagocytose host cells validates the previously published microarray data set demonstrating feed-forward control of E. histolytica phagocytosis. Finally, although only limited conclusions can be drawn from studies using the virulence-deficient G3 Entamoeba strain, the relative specificity of the defects induced for phagocytosis of apoptotic cells but not healthy cells suggests that cell killing may play a rate-limiting role in the process of Entamoeba histolytica host cell engulfment.

A Fluorescent Reporter for Single Cell Analysis of Gene Expression in Clostridium difficile

Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O ( 6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O ( 6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O ( 6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.

The past, present and future of fluorescent protein tags in anaerobic protozoan parasites

The world health organization currently recognizes diarrhoeal diseases as a significant cause of death in children globally. Protozoan parasites such as Giardia and Entamoeba that thrive in the oxygen-deprived environment of the human gut are common etiological agents of diarrhoea. In the urogenital tract of humans, the anaerobic protozoan parasite Trichomonas vaginalis is notorious as the most common non-viral, sexually transmitted pathogen. Even with high medical impact, our understanding of anaerobic parasite physiology is scarce and as a result, treatment choices are limited. Fluorescent proteins (FPs) are invaluable tools as genetically encoded protein tags for advancing knowledge of cellular function. These FP tags emit fluorescent colours and once attached to a protein of interest, allow tracking of parasite proteins in the dynamic cellular space. Application of green FPs-like FPs in anaerobic protozoans is hindered by their oxygen dependency. In this review, we examine aspects of anaerobic parasite biology that clash with physio-chemical properties of FPs and limit their use as live-parasite protein tags. We expose novel FPs, such as miniSOG that do not require oxygen for signal production. The potential use of novel FPs has the opportunity to leverage the anaerobe parasitologist toolkit to that of aerobe parasitologist.

Live-cell reporters for fluorescence imaging

Advances in the development of new fluorescent reporters and imaging techniques have revolutionized our ability to directly visualize biological processes in living systems. Real-time analysis of protein localization, dynamics, and interactions has been made possible by site-specific protein labeling with custom designed probes. This review outlines some of the most recent advances in the design and application of live-cell imaging probes, with a particular focus on SNAP-tag technology. Specific examples illustrating applications in superresolution and single-molecule imaging, protein trafficking and recycling, and protein-protein interactions are presented.