Fungal Endosymbiosis and Pathogenicity 3 4 Herbert Itabangi1, Poppy C

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Fungal Endosymbiosis and Pathogenicity 3 4 Herbert Itabangi1, Poppy C bioRxiv preprint doi: https://doi.org/10.1101/584607; this version posted December 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Environmental interactions with amoebae as drivers of bacterial- 2 fungal endosymbiosis and pathogenicity 3 4 Herbert Itabangi1, Poppy C. S. Sephton-Clark1, Xin Zhou1, Georgina P. Starling2, Zamzam 5 Mahamoud2, Ignacio Insua3, Mark Probert1, Joao Correia1, Patrick J. Moynihan1, Teklegiorgis 6 Gebremariam4, Yiyou Gu4, Ashraf S. Ibrahim4,5, Gordon D. Brown6, Jason S. King2*, Elizabeth 7 R. Ballou1* and Kerstin Voelz1* 8 1Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, 9 Edgbaston, Birmingham, B15 2TT, UK. 10 2Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 11 2TN, UK. 12 3School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. 13 4 The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, 14 Torrance, California, U.S.A. 15 5David Geffen School of Medicine, UCLA, Los Angeles, California, U.S.A. 16 6 MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, 17 Stocker Road, Exeter, EX4 4QD 18 19 * To whom correspondence should be addressed 20 JSK: [email protected] 21 ERB: [email protected] 22 KV: [email protected] 23 24 25 Keywords: Murcomycete, Rhizopus, Ralstonia, Dictyostelium, endosymbiosis, evolution, soil 26 microbiology 27 1 bioRxiv preprint doi: https://doi.org/10.1101/584607; this version posted December 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract 2 Opportunistic infections by environmental fungi are a growing clinical problem, driven by an 3 increasing population of people with immunocompromising conditions. Spores of the 4 Mucorales order are ubiquitious in the environment but can also cause acute invasive infections 5 in humans through germination and evasion of the mammalian host immune system. How they 6 achieve this, and the evolutionary drivers underlying the acquisition of virulence mechanisms, 7 are poorly understood. Here we show that a clinical isolate of Rhizopus microsporus contains 8 a Ralstonia pickettii bacterial endosymbiont required for virulence in both zebrafish and mice, 9 and that this endosymbiosis enables secretion of factors that potently suppress growth of the 10 soil amoeba Dictyostelium discoideum, as well as their ability to engulf and kill other microbes. 11 As amoebae are natural environmental predators of both bacteria and fungi, we propose this 12 tri-kingdom interaction contributes to establishing the endosymbiosis, and acquisition of anti- 13 phagocyte activity. Importantly, we show this activity also protects fungal spores from 14 phagocytosis and clearance by human macrophages, and endosymbiont removal renders the 15 fungal spores avirulent in vivo. Together, these findings describe a novel role for a bacterial 16 endosymbiont in Rhizopus microsporus pathogenesis in animals, and suggest a mechanism of 17 virulence acquisition through environmental interactions with amoebae. 18 In brief 19 How environmental fungi evolved the mechanisms that enable them to cause opportunistic 20 infections in humans is unclear. Here, we identify a novel tri-kingdom interaction, whereby a 21 bacterial endosymbiont, living within a clinical isolate of the ubiquitous environmental 22 fungus Rhizopus microsporus, causes the generation of a secreted activity that blocks the 23 growth and predatory activity of amoebae. We suggest this provides a new evolutionary 24 driver for the establishment of bacterial/fungal endosymbiosis and demonstrate this is critical 25 for fungal pathogenicity in vivo. 2 bioRxiv preprint doi: https://doi.org/10.1101/584607; this version posted December 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Introduction 2 Soil-dwelling fungi must evade predation by phagocytic amoebae and, similarly, pathogenic 3 fungi evade host phagocytic cells that defend against infection (1, 2). Interaction with amoebae 4 has been proposed as an evolutionary training ground for pathogenic fungi, enabling them to 5 resist the multifactorial stresses of the mammalian host. Mucoralean fungi such as soil- 6 associated Rhizopus microsporus, which causes invasive mucormycosis, successfully establish 7 in complex polymicrobial environments that include predatory amoeba. Yet, they lack common 8 strategies fungi employ to evade predation and phagocytosis: R. microsporus fails to mask cell 9 wall ligands in swollen spores, has a slow germination rate, and produces relatively low 10 biomass (3, 4). Mucorales resting spores also fail to elicit pro-inflammatory cytokine responses 11 and do not induce strong phagocyte chemotaxis. Here, we investigate an as yet unexplored 12 aspect of R. microsporus pathogen biology: the impact of a bacterial endosymbiont on 13 interaction with amoebae and host phagocytes. 14 Pathogenic Mucorales span multiple genera, with the Rhizopus genus causing almost 15 half of all documented cases and high mortality in susceptible patient populations (5-12). 16 Infection occurs through inoculation with dormant, immunologically inert spores. Upon 17 germination, these spores become metabolically active and begin to swell (13, 14). Based on 18 analogy to Aspergillus spores, frequently used as a model for Mucorales, swelling is expected 19 to reveal Microbe Associated Molecular Patterns (MAMPs) and induce increasing rates of 20 phagocytosis which must be overcome by rapid hyphal extension (15, 16). However, swollen 21 spores in the Rhizopus genus are often no more readily phagocytosed than resting spores and 22 R. microsporus spores are phagocytosed at lower rates than other well studied fungal spores 23 (17-20). While in some species, larger spore size (12.3 µm) reduces phagocytosis, the small 24 spore size of R. microscoprus (5 µm, comparable to other well-phagocytosed particles) makes 25 this unlikely to explain the observed reduced uptake (21, 22). 26 A common strategy fungi employ to evade phagocytosis is through masking cell wall 27 ligands (16, 23-28). Two classic examples of this are the Cryptococcus neoformans capsule 28 and the Aspergillus spore hydrophobin layer, which effectively block phagocytosis by 29 preventing detection of MAMPs (15, 16, 27-30). However, there is no evidence of 30 hydrophobins in the R. microsporus genome, and evidence of cell wall remodelling that masks 31 MAMPs is limited to the hyphal phase (31). Moreover, R. microsporus has a slow germination 32 rate, and produces relatively low biomass, which are predicted to reduce fungal virulence (3, 3 bioRxiv preprint doi: https://doi.org/10.1101/584607; this version posted December 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 4, 21, 32-34). Together, these differences suggest an alternate strategy available to Rhizopus 2 for the evasion of phagocytosis during the early stages of germination. 3 4 Mucormycete plant pathogens, including the Mucorales, are frequently colonized or 5 influenced by bacteria of the genera Burkholderia, Paraburholderia, and Ralstonia, all closely 6 related to the Pseudomonas genus (35-37). During endosymbiosis, Burkholderia spp. influence 7 fungal behaviour such as growth and sporulation, and also mediate plant pathogenesis (37, 38). 8 For example, the endotoxin Rhizoxin is secreted by Burkholderia rhizoxina during mutualism 9 with R. microsporus and inhibits plant defences (39, 40). The Ralstonia solanacearum 10 lipopeptide ralsolamycin can influence chlamydospore development and hyphal invasion (37). 11 While endosymbionts are widespread in patient fungal samples, a role for endosymbionts in 12 preventing fungal phagocytosis has not been established (35). Rather, work examining this 13 interaction in the context of phagocyte-deficient mouse models found no correlation between 14 endosymbiont presence and fungal virulence (35). We recently showed that phagocyte activity 15 in the early stages of infection control are critical for predicting Mucorales disease outcome, 16 suggesting that phagocyte-deficiency primes the host for infection (41). Together, this raises 17 the hypothesis: do endosymbionts specifically impact fungal interaction with phagocytic cells, 18 including both environmental amoebae and mammalian macrophages and neutrophils, leading 19 to enhanced fungal virulence? 20 21 Here, we investigate the interaction of environmental and early host phagocytic cells with R. 22 microsporus. We report, for the first time, a role for a bacterial endosymbiont of R. 23 microsporus in modulating the interaction with these phagocytic cells and further expand this 24 to demonstrate a role in the early stages of disease in both zebrafish and murine models of 25 infection.
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