Observations with Hoechst Staining of Amitosis inAcanthamoeba castellanii

Phylogenomic, structural, and cell biological analyses reveal that Stenotrophomonas maltophilia replicates in acidified Rab7A-positive vacuoles of Acanthamoeba castellanii

Acanthamoeba species are clinically relevant free-living amoebae (FLA) ubiquitously found in soil and water bodies. Metabolically active trophozoites graze on diverse microbes via phagocytosis. However, functional studies on Rab GTPases (Rabs), which are critical for controlling vesicle trafficking and maturation, are scarce for this FLA. This knowledge gap can be partly explained by the limited genetic tools available for Acanthamoeba cell biology. Here, we developed plasmids to generate fusions of A. castellanii strain Neff proteins to the N- or C-termini of mEGFP and mCherry2. Phylogenomic and structural analyses of the 11 Neff Rab7 paralogs found in the RefSeq assembly revealed that eight of them had non-canonical sequences. After correcting the gene annotation for the Rab7A ortholog, we generated a line stably expressing an mEGFP-Rab7A fusion, demonstrating its correct localization to acidified macropinocytic and phagocytic vacuoles using fluorescence microscopy live cell imaging (LCI). Direct labeling of live Stenotrophomonas maltophilia ESTM1D_MKCAZ16_6a (Sm18) cells with pHrodo Red, a pH-sensitive dye, demonstrated that they reside within acidified, Rab7A-positive vacuoles. We constructed new mini-Tn7 delivery plasmids and tagged Sm18 with constitutively expressed mScarlet-I. Co-culture experiments of Neff trophozoites with Sm18::mTn7TC1_Pc_mScarlet-I, coupled with LCI and microplate reader assays, demonstrated that Sm18 underwent multiple replication rounds before reaching the extracellular medium via non-lytic exocytosis. We conclude that S. maltophilia belongs to the class of bacteria that can use amoeba as an intracellular replication niche within a Stenotrophomonas-containing vacuole that interacts extensively with the endocytic pathway.IMPORTANCEDiverse Acanthamoeba lineages (genotypes) are of increasing clinical concern, mainly causing amoebic keratitis and granulomatous amebic encephalitis among other infections. S. maltophilia ranks among the top 10 most prevalent multidrug-resistant opportunistic nosocomial pathogens and is a recurrent member of the microbiome hosted by Acanthamoeba and other free-living amoebae. However, little is known about the molecular strategies deployed by Stenotrophomonas for an intracellular lifestyle in amoebae and other professional phagocytes such as macrophages, which allow the bacterium to evade the immune system and the action of antibiotics. Our plasmids and easy-to-use microtiter plate co-culture assays should facilitate investigations into the cellular microbiology of Acanthamoeba interactions with Stenotrophomonas and other opportunistic pathogens, which may ultimately lead to the discovery of new molecular targets and antimicrobial therapies to combat difficult-to-treat infections caused by these ubiquitous microbes.

Genetic manipulation of giant viruses and their host, Acanthamoeba castellanii

Giant viruses (GVs) provide an unprecedented source of genetic innovation in the viral world and are thus, besides their importance in basic and environmental virology, in the spotlight for bioengineering advances. Their host, Acanthamoeba castellanii, is an accidental human pathogen that acts as a natural host and environmental reservoir of other human pathogens. Tools for genetic manipulation of viruses and host were lacking. Here, we provide a detailed method for genetic manipulation of A. castellanii and the GVs it plays host to by using CRISPR-Cas9 or homologous recombination. We detail the steps of vector preparation (4 d), transfection of amoeba cells (1 h), infection (1 h), selection (5 d for viruses, 2 weeks for amoebas) and cloning of recombinant viruses (4 d) or amoebas (2 weeks). This procedure takes ~3 weeks or 1 month for the generation of recombinant viruses or amoebas, respectively. This methodology allows the generation of stable gene modifications, which was not possible by using RNA silencing, the only previously available reverse genetic tool. We also include detailed sample-preparation steps for protein localization by immunofluorescence (4 h), western blotting (4 h), quantification of viral particles by optical density (15 min), calculation of viral lethal dose 50 (7 d) and quantification of DNA replication by quantitative PCR (4 h) to allow efficient broad phenotyping of recombinant organisms. This methodology allows the function of thousands of ORFan genes present in GVs, as well as the complex pathogen-host, pathogen-pathogen or pathogen-symbiont interactions in A. castellanii, to be studied in vivo.

Evolution of giant pandoravirus revealed by CRISPR/Cas9

Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of "Virus" and their origin. While increasing knowledge of genome diversity has accumulated, GV functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and their host Acanthamoeba castellanii using CRISPR/Cas9, shedding light on the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the phylogenetically-related mollivirus highlights a transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. This proposed genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and provide experimental evidence suggesting that viral gigantism has aroused as an emerging trait.

Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.

Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single-cell level

Amitosis is widespread among eukaryotes, but the underlying mechanisms are poorly understood. The polyploid macronucleus (MAC) of unicellular ciliates divides by amitosis, making ciliates a potentially valuable model system to study this process. However, a method to accurately quantify the copy number of MAC chromosomes has not yet been established. Here we used droplet digital PCR (ddPCR) to quantify the absolute copy number of the MAC chromosomes in Tetrahymena thermophila. We first confirmed that ddPCR is a sensitive and reproducible method to determine accurate chromosome copy numbers at the single-cell level. We then used ddPCR to determine the copy number of different MAC chromosomes by analyzing individual T. thermophila cells in the G1 and the amitotic (AM) phases. The average copy number of MAC chromosomes was 90.9 at G1 phase, approximately half the number at AM phase (189.8). The copy number of each MAC chromosome varied among individual cells in G1 phase and correlated with cell size, suggesting that amitosis accompanied by unequal cytokinesis causes copy number variability. Furthermore, the fact that MAC chromosome copy number is less variable among AM-phase cells suggests that the copy number is standardized by regulating DNA replication. We also demonstrated that copy numbers differ among different MAC chromosomes and that interchromosomal variations in copy number are consistent across individual cells. Our findings demonstrate that ddPCR can be used to model amitosis in T. thermophila and possibly in other ciliates.

Limitations of the Human-PBL-SCID Mouse Model for Vaginal Transmission of HIV-1

PROBLEM

SCID mice reconstituted with human peripheral blood lymphocytes (PBL) are amenable to vaginal transmission of HIV-1. We investigated the effectiveness of this model to establish systemic HIV-1 infection.

METHOD OF STUDY

Eighty progesterone-primed C.B-17 SCID mice were reconstituted with human-PBLs and intravaginally inoculated with CCR5 HIV-1 (BaL or 92BR09) infected human-PBLs in the presence of human semen. After two weeks, viral RNA load in spleen, peritoneal lavage (PL), and serum was quantitated by the nucleic acid sequence-based amplification method.

RESULTS

In five independent experiments, spleen from 8/60 (13.3%), PL from 7/60 (11.6%), and serum from 16/56 (28.5%) mice were positive for BaL HIV-1 infection. Similarly, spleen from 4/20 (20%), PL from 1/20 (5%) and serum from 5/20 (25%) mice vaginally inoculated with 92BR09-infected human-PBLs were positive for HIV-1. A one-sided power analysis using normal approximation revealed that at 5% significance level, the overall response rate need to increase form 0.29 to 0.9 and 80% of the control groups needs to achieve a response rate between 6/10 and 9/10 to make the assay feasible.

CONCLUSION

The incidence of vaginal transmission of CCR5 HIV-1 in the human-PBL-SCID mouse was low and variable, which constitutes a major disadvantage for preclinical evaluation of vaginal microbicides.

Pneumocystis carinii cysts are susceptible to inactivation by chemical disinfectants

The inactivation efficacy of eight disinfectants commonly used in laboratories and animal rooms to inactive Pneumocystis carinii cysts was estimated by experimental infection in C.B-17-scid mice. The disinfectants examined in this study were 70% ethyl alcohol, 10% iodoform, 0.5% hypochlorous acid, two 1% quanternary ammonium salts, 3% hydrogen peroxide, sodium chlorite and 1% cresol soap. The lung homogenates from P. carinii infected C.B-17-scid mice were treated with each disinfectant for 15 min at room temperature, washed with saline, and inoculated into C.B-17-scid mice. Eight weeks after inoculation, lungs from these mice were examined by staining with toluidine blue O to detect P. carinii cysts. PCR amplifying 346 bp of P. carinii specific mitochondrial ribosomal RNA large segments was also performed using DNA extracted from the lungs of the mice. As a result, seven disinfectants, excepting for 0.5% hypochlorous acid, were effective in the inactivation of P. carinii cysts. These results suggest that P. carinii cysts were sensitive to chemical disinfectants even though they have been commonly considered as insensitive.

Cytological and immunocytochemical approaches to the study of corneal endothelial wound repair

The vertebrate corneal endothelium represents a unique model system for investigating many cellular aspects of wound repair within an organized tissue in situ. The tissue exists as a cell monolayer that resides upon its own natural basement membrane that can be prepared as a flat mount to observe the entire cell population. Thus, it readily avails itself to many cytological and immunocytochemical methods at both the light microscopic and ultrastructural levels. In addition, the tissue is easily explanted into organ culture where further investigations can be carried out. These techniques have enabled investigators to use many approaches to explore function and changes in response to injury. In vivo, the endothelium acts as a transport tissue to actively pump Na+ and bicarbonate ions from the corneal stroma into the aqueous humor to control corneal transparency. Physiological findings indicate that fluid diffuses back into the stroma, across the endothelium, and thus hydration is said to be controlled by a pump-leak mechanism. Ultrastructural investigations, some employing horseradish peroxidase and lanthanum, have established the morphological basis for this mechanism as apical focal junctions that are not the classical tight junctions and do not constitute a complete zona occludens. Along with these apical focal junctions are gap junctions that appear identical to their counterparts in other cell types. Cytochemical studies localized both Na+K(+)-ATPase and carbonic anhydrase, the main pump enzymes associated with corneal hydration, to the lateral plasma membranes. Corneal endothelial cells of noninjured tissue do not traverse the cell cycle and are considered to be in the "Go" phase of the cell cycle as determined by microfluorometric analysis with DNA binding dyes such as auramin O and pararosaniline-Feulgen. However, injury can initiate cell cycle transverse and histochemical and cytological methods have been used to understand the tissue's response. Classical histochemical studies revealed that increased staining was observed for metabolic (NADase and NADPase) and lysosomal enzymes in cells bordering the wound area. The use of radiolabelled agents has further lead to an understanding of the endothelial wound response. Autoradiographic analyses of 3H-actinomycin D incorporation indicated that injury initiates changes in chromatin leading to increased binding levels of the drug in cells surrounding the wound. This change suggests that those cells undergo heightened macromolecular synthesis and this was confirmed by examining 3H-uridine and 3H-thymidine incorporation. The major mechanism involved in corneal endothelial repair is cell migration. Cytochemical and immunocytochemical investigations have allowed investigators an opportunity to gain some insight into changes that occur during this cellular process.(ABSTRACT TRUNCATED AT 400 WORDS)