Browsing by Author "Heunis, Tiaan"

Now showing 1 - 4 of 4
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    Comprehensive characterization of the attenuated double auxotroph mycobacterium tuberculosisΔleuDΔpanCD as an alternative to H37Rv
    (Frontiers Media, 2019) Mouton, Jomien M.; Heunis, Tiaan; Dippenaar, Anzaan; Gallant, James L.; Kleynhans, Leanie; Sampson, Samantha L.
    ENGLISH ABSTRACT: Although currently available model organisms such as Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) have significantly contributed to our understanding of tuberculosis (TB) biology, these models have limitations such as differences in genome size, growth rates and virulence. However, attenuated Mycobacterium tuberculosis strains may provide more representative, safer models to study M. tuberculosis biology. For example, the M. tuberculosis ΔleuDΔpanCD double auxotroph, has undergone rigorous in vitro and in vivo safety testing. Like other auxotrophic strains, this has subsequently been approved for use in biosafety level (BSL) 2 facilities. Auxotrophic strains have been assessed as models for drug-resistant M. tuberculosis and for studying latent TB. These offer the potential as safe and useful models, but it is important to understand how well these recapitulate salient features of non-attenuated M. tuberculosis. We therefore performed a comprehensive comparison of M. tuberculosis H37Rv and M. tuberculosisΔleuDΔpanCD. These strains demonstrated similar in vitro and intra-macrophage replication rates, similar responses to anti-TB agents and whole genome sequence conservation. Shotgun proteomics analysis suggested that M. tuberculosisΔleuDΔpanCD has a heightened stress response that leads to reduced bacterial replication during exposure to acid stress, which has been verified using a dual-fluorescent replication reporter assay. Importantly, infection of human peripheral blood mononuclear cells with the 2 strains elicited comparable cytokine production, demonstrating the suitability of M. tuberculosisΔleuDΔpanCD for immunological assays. We provide comprehensive evidence to support the judicious use of M. tuberculosisΔleuDΔpanCD as a safe and suitable model organism for M. tuberculosis research, without the need for a BSL3 facility.
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    Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics
    (BioMed Central, 2020-03-23) Kriel, Nastassja L.; Heunis, Tiaan; Sampson, Samantha L.; Gey Van Pittius, Nico C.; Williams, Monique J.; Warren, Robin M.
    Background: Transcriptional responses required to maintain cellular homeostasis or to adapt to environmental stress, is in part mediated by several nucleic-acid associated proteins. In this study, we sought to establish an affinity purification-mass spectrometry (AP-MS) approach that would enable the collective identification of nucleic acidassociated proteins in mycobacteria. We hypothesized that targeting the RNA polymerase complex through affinity purification would allow for the identification of RNA- and DNA-associated proteins that not only maintain the bacterial chromosome but also enable transcription and translation. Results: AP-MS analysis of the RNA polymerase β-subunit cross-linked to nucleic acids identified 275 putative nucleic acid-associated proteins in the model organism Mycobacterium smegmatis under standard culturing conditions. The AP-MS approach successfully identified proteins that are known to make up the RNA polymerase complex, as well as several other known RNA polymerase complex-associated proteins such as a DNA polymerase, sigma factors, transcriptional regulators, and helicases. Gene ontology enrichment analysis of the identified proteins revealed that this approach selected for proteins with GO terms associated with nucleic acids and cellular metabolism. Importantly, we identified several proteins of unknown function not previously known to be associated with nucleic acids. Validation of several candidate nucleic acid-associated proteins demonstrated for the first time DNA association of ectopically expressed MSMEG_1060, MSMEG_2695 and MSMEG_4306 through affinity purification. Conclusions: Effective identification of nucleic acid-associated proteins, which make up the RNA polymerase complex as well as other DNA- and RNA-associated proteins, was facilitated by affinity purification of the RNA polymerase β- subunit in M. smegmatis. The successful identification of several transcriptional regulators suggest that our approach could be sensitive enough to investigate the nucleic acid-associated proteins that maintain cellular functions and mediate transcriptional and translational change in response to environmental stress.
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    ProVision: A web based platform for rapid analysis of proteomics data processed by MaxQuant
    (2020-07) Gallant, James; Heunis, Tiaan; Sampson, Samantha Leigh; Bitter, Wilbert
    Proteomics is a powerful tool for protein expression analysis and is becoming more readily available to researchers through core facilities or specialised collaborations. However, one major bottleneck for routine implementation and accessibility of this technology to the wider scientific community is the complexity of data analysis. To this end, we have created ProVision, a free open-source web-based analytics platform that allows users to analyse data from two common proteomics relative quantification workflows, namely label-free and tandem mass tag-based experiments. Furthermore, ProVision allows the freedom to interface with the data analysis pipeline while maintaining a user-friendly environment and providing default parameters for fast statistical and exploratory data analysis. Finally, multiple customisable quality control, differential expression plots as well as enrichments and protein-protein interaction prediction can be generated online in one platform. Availability and implementation: Quick start and step-by-step tutorials as well as tutorial data is fully incorporated in the web application. This application is available online at https://provision.shinyapps.io/provision/ for free use. The source code is available at https://github.com/JamesGallant/ProVision under the GPL version 3.0 license.
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    Release of bacteriocins from nanofibers prepared with combinations of poly(D,L-lactide) (PDLLA) and poly(ethylene oxide) (PEO)
    (MDPI, 2011) Heunis, Tiaan; Bshena, Osama; Klumperman, Bert; Dicks, Leon Milner Theodore, 1961-
    Plantaricin 423, produced by Lactobacillus plantarum, and bacteriocin ST4SA produced by Enterococcus mundtii, were electrospun into nanofibers prepared from different combinations of poly(D,L-lactide) (PDLLA) and poly(ethylene oxide) (PEO) dissolved in N,N-dimethylformamide (DMF). Both peptides were released from the nanofibers with a high initial burst and retained 88% of their original antimicrobial activity at 37 °C. Nanofibers have the potential to serve as carrier matrix for bacteriocins and open a new field in developing controlled antimicrobial delivery systems for various applications.