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Wen XF, Shi TT, Zhang YQ, Wang SH, Xiang CM, Zhao PJ. DHXT1, a Virulence Factor of Dactylellina haptotyla, Regulates Pathogenicity by Participating in Trap Formation and Metabolite Synthesis. Int J Mol Sci 2024; 25:7384. [PMID: 39000488 PMCID: PMC11242603 DOI: 10.3390/ijms25137384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
The capsule-associated protein 10 gene (CAP10) is indispensable due to its involvement in pod formation and virulence maintenance in Cryptococcus neoformans. The function of the CAP10 gene in nematode-predatory fungi remains unreported. As a typical nematode-trapping fungus, Dactylellina haptotyla efficiently captures nematodes using adhesive knobs, which has potential applications in the biological control of plant-parasitic nematodes. In this study, we investigated the function of DHXT1 (a CAP10 homologous protein) in D. haptotyla-nematode interactions based on the disruption and overexpression of DHXT1, phenotypic analysis and metabolomic analysis. As a result, it was shown that the disruption of the DHXT1 gene causes a marked decrease in the number of adhesive knobs, and on the contrary, the overexpression of the DHXT1 gene causes a substantial increase in the number of adhesive knobs. Interestingly, the variety of metabolites increased with the disruption of the DHXT1 and decreased with the overexpression of the DHXT1 gene. The results suggest that DHXT1 effects pathogenicity through its involvement in adhesive knobs' formation and metabolite synthesis and serves as a key virulence factor in D. haptotyla.
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Affiliation(s)
| | | | | | | | | | - Pei-Ji Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China; (X.-F.W.); (T.-T.S.); (Y.-Q.Z.); (S.-H.W.); (C.-M.X.)
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2
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Conn BN, Lieberman JA, Chatman P, Cotton K, Essandoh MA, Ebqa’ai M, Nelson TL, Wozniak KL. Antifungal activity of eumelanin-inspired indoylenepheyleneethynylene against Cryptococcus neoformans. Front Microbiol 2024; 14:1339303. [PMID: 38293553 PMCID: PMC10826398 DOI: 10.3389/fmicb.2023.1339303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that causes meningitis in >152,000 immunocompromised individuals annually, leading to 112,000 yearly deaths. The four classes of existing antifungal agents target plasma membrane sterols (ergosterol), nucleic acid synthesis, and cell wall synthesis. Existing drugs are not highly effective against Cryptococcus, and antifungal drug resistance is an increasing problem. A novel antimicrobial compound, a eumelanin-inspired indoylenepheyleneethynylene, EIPE-1, was synthesized and has antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MSRA), but not towards Gram-negative organisms. Based on EIPE-1's antibacterial activity, we hypothesized that EIPE-1 could have antifungal activity. For these studies, we tested EIPE-1 against C. neoformans strain H99 and 6 additional cryptococcal clinical isolates. We examined antifungal activity, cytotoxicity, effects on fungal gene expression, and mechanism of action of EIPE-1. Results showed that EIPE-1 has fungicidal effects on seven cryptococcal strains with MICs ranging from 1.56 to 3.125 μg/mL depending on the strain, and it is non-toxic to mammalian cells. We conducted scanning and transmission electron microscopy on the exposed cells to examine structural changes to the organism following EIPE-1 treatment. Cells exposed displayed structural changes to their cell wall and membranes, with internal contents leaking out of the cells. To understand the effect of EIPE-1 on fungal gene expression, RNA sequencing was conducted. Results showed that EIPE-1 affects several processes involved stress response, ergosterol biosynthesis, capsule biosynthesis, and cell wall attachment and remodeling. Therefore, our studies demonstrate that EIPE-1 has antifungal activity against C. neoformans, which affects both cellular structure and gene expression of multiple fungal pathways involved in cell membrane stability and viability.
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Affiliation(s)
- Brittney N. Conn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Jacob A. Lieberman
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Priscilla Chatman
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Kaitlyn Cotton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Martha A. Essandoh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Mohammad Ebqa’ai
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Toby L. Nelson
- Department of Chemistry, Oklahoma State University, Stillwater, OK, United States
| | - Karen L. Wozniak
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
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3
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Ullah A, Huang Y, Zhao K, Hua Y, Ullah S, Rahman MU, Wang J, Wang Q, Hu X, Zheng L. Characteristics and potential clinical applications of the extracellular vesicles of human pathogenic Fungi. BMC Microbiol 2023; 23:227. [PMID: 37598156 PMCID: PMC10439556 DOI: 10.1186/s12866-023-02945-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/14/2023] [Indexed: 08/21/2023] Open
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of lipid membrane-enclosed compartments that contain different biomolecules and are released by almost all living cells, including fungal genera. Fungal EVs contain multiple bioactive components that perform various biological functions, such as stimulation of the host immune system, transport of virulence factors, induction of biofilm formation, and mediation of host-pathogen interactions. In this review, we summarize the current knowledge on EVs of human pathogenic fungi, mainly focusing on their biogenesis, composition, and biological effects. We also discuss the potential markers and therapeutic applications of fungal EVs.
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Affiliation(s)
- Amir Ullah
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yiyi Huang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Kening Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Yuneng Hua
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shafi Ullah
- Department of pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Mujeeb Ur Rahman
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jingyu Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Qian Wang
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
| | - Xiumei Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
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4
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Jang EH, Kim JS, Yu SR, Bahn YS. Unraveling Capsule Biosynthesis and Signaling Networks in Cryptococcus neoformans. Microbiol Spectr 2022; 10:e0286622. [PMID: 36287085 PMCID: PMC9769619 DOI: 10.1128/spectrum.02866-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 01/09/2023] Open
Abstract
The polysaccharide capsule of Cryptococcus neoformans-an opportunistic basidiomycete pathogen and the major etiological agent of fungal meningoencephalitis-is a key virulence factor that prevents its phagocytosis by host innate immune cells. However, the complex signaling networks for their synthesis and attachment remain elusive. In this study, we systematically analyzed capsule biosynthesis and signaling networks using C. neoformans transcription factor (TF) and kinase mutant libraries under diverse capsule-inducing conditions. We found that deletion of GAT201, YAP1, BZP4, and ADA2 consistently caused capsule production defects in all tested media, indicating that they are capsule-regulating core TFs. Epistatic and expression analyses showed that Yap1 and Ada2 control Gat201 upstream, whereas Bzp4 and Gat201 independently regulate capsule production. Next, we searched for potential upstream kinases and found that mutants lacking PKA1, BUD32, POS5, IRE1, or CDC2801 showed reduced capsule production under all three capsule induction conditions, whereas mutants lacking HOG1 and IRK5 displayed enhanced capsule production. Pka1 and Irk5 controlled the induction of GAT201 and BZP4, respectively, under capsule induction conditions. Finally, we monitored the transcriptome profiles governed by Bzp4, Gat201, and Ada2 under capsule-inducing conditions and demonstrated that these TFs regulate redundant and unique sets of downstream target genes. Bzp4, Ada2, and Gat201 govern capsule formation in C. neoformans by regulating the expression of various capsule biosynthesis genes and chitin/chitosan synthesis genes in a positive and negative manner, respectively. In conclusion, this study provides further insights into the complex regulatory mechanisms of capsule production-related signaling pathways in C. neoformans. IMPORTANCE Over the past decades, human fungal pathogens, including C. neoformans, have emerged as a major public threat since the AIDS pandemic, only to gain more traction in connection to COVID-19. Polysaccharide capsules are rare fungal virulence factors that are critical for protecting C. neoformans from phagocytosis by macrophages. To date, more than 75 proteins involved in capsule synthesis and cell wall attachment have been reported in C. neoformans; however, their complex upstream signaling networks remain elusive. In this study, we demonstrated that Ada2, Yap1, Bzp4, and Gat201 were key capsule-inducing transcriptional regulators. Yap1 and Ada2 function upstream of Gat201, whereas Bzp4 and Gat201 function independently. Genome-wide transcriptome profiling revealed that Bzp4, Gat201, and Ada2 promote capsule production and attachment by positively and negatively regulating genes involved in capsule synthesis and chitin/chitosan synthesis, respectively. Thus, this study provides comprehensive insights into the complex capsule-regulating signaling pathway in C. neoformans.
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Affiliation(s)
- Eun-Ha Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji-Seok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Seong-Ryong Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
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5
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Rizzo J, Wong SSW, Gazi AD, Moyrand F, Chaze T, Commere P, Novault S, Matondo M, Péhau‐Arnaudet G, Reis FCG, Vos M, Alves LR, May RC, Nimrichter L, Rodrigues ML, Aimanianda V, Janbon G. Cryptococcus extracellular vesicles properties and their use as vaccine platforms. J Extracell Vesicles 2021; 10:e12129. [PMID: 34377375 PMCID: PMC8329992 DOI: 10.1002/jev2.12129] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting-edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein-based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analysing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane-bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.
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Affiliation(s)
- Juliana Rizzo
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Sarah Sze Wah Wong
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Anastasia D. Gazi
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Frédérique Moyrand
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Thibault Chaze
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Pierre‐Henri Commere
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Sophie Novault
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Gérard Péhau‐Arnaudet
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Flavia C. G. Reis
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Centro de Desenvolvimento Tecnologico em Saude (CDTS‐Fiocruz)São PauloBrazil
| | - Matthijn Vos
- NanoImaging Core FacilityCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | | | - Robin C. May
- Institute of Microbiology and Infection and School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Marcio L. Rodrigues
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Vishukumar Aimanianda
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
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6
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Extracellular Vesicles in the Fungi Kingdom. Int J Mol Sci 2021; 22:ijms22137221. [PMID: 34281276 PMCID: PMC8269022 DOI: 10.3390/ijms22137221] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/14/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous, rounded vesicles released by prokaryotic and eukaryotic cells in their normal and pathophysiological states. These vesicles form a network of intercellular communication as they can transfer cell- and function-specific information (lipids, proteins and nucleic acids) to different cells and thus alter their function. Fungi are not an exception; they also release EVs to the extracellular space. The vesicles can also be retained in the periplasm as periplasmic vesicles (PVs) and the cell wall. Such fungal vesicles play various specific roles in the lives of these organisms. They are involved in creating wall architecture and maintaining its integrity, supporting cell isolation and defence against the environment. In the case of pathogenic strains, they might take part in the interactions with the host and affect the infection outcomes. The economic importance of fungi in manufacturing high-quality nutritional and pharmaceutical products and in remediation is considerable. The analysis of fungal EVs opens new horizons for diagnosing fungal infections and developing vaccines against mycoses and novel applications of nanotherapy and sensors in industrial processes.
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7
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Cryptococcus neoformans CAP10 Gene Regulates the Immune Response in Mice. J Mycol Med 2021; 31:101160. [PMID: 34311225 DOI: 10.1016/j.mycmed.2021.101160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/22/2022]
Abstract
The capsule associated protein 10 gene (CAP10) is indispensable to the formation of the polysaccharide capsule, and is closely associated with Cryptococcus (C.) neoformans virulence. In this study, we designed the shRNA expression plasmid to interfere with the synthesis of CAP10 gene. We infected mice with yeast cells in the respiratory tract, and monitored the development of infections in lung tissues. Results showed that the cap10-shRNA group may alleviate pathological lesions in pulmonary C. neoformans infection, and a lower degree of inflammatory cells was observed in the cap10-shRNA group. Moreover, the fungal burden was significantly lower in the cap10-shRNA group, indicating that the clearance towards C. neoformans was somehow affected. Down-regulation of CAP10 was beneficial to the balance of Th1/Th2 and Th17/Treg ratios. Collectively, our results showed that the expression of CAP10 was associated with an antifungal immune response in mice, suggesting that CAP10 regulates the inflammatory response. Therefore, we expect that the CAP10 gene will become a new molecular therapeutic target in cryptococcosis treatment.
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8
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Bakuła Z, Siedlecki P, Gromadka R, Gawor J, Gromadka A, Pomorski JJ, Panagiotopoulou H, Jagielski T. A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. BMC Genomics 2021; 22:168. [PMID: 33750287 PMCID: PMC7941945 DOI: 10.1186/s12864-021-07491-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529. RESULTS The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome. CONCLUSIONS Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Paweł Siedlecki
- Department of Systems Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.,Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan J Pomorski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.
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9
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Roth C, Murray D, Scott A, Fu C, Averette AF, Sun S, Heitman J, Magwene PM. Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PLoS Genet 2021; 17:e1009313. [PMID: 33493169 PMCID: PMC7861560 DOI: 10.1371/journal.pgen.1009313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 12/17/2020] [Indexed: 01/11/2023] Open
Abstract
Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of Cryptococcus deneoformans, which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent C. deneoformans strains. Using a "function-valued" QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes, RIC8, which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes SSK1 and SSK2, which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of Cryptococcus, and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.
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Affiliation(s)
- Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alexandria Scott
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna F. Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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10
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Gerstein AC, Jackson KM, McDonald TR, Wang Y, Lueck BD, Bohjanen S, Smith KD, Akampurira A, Meya DB, Xue C, Boulware DR, Nielsen K. Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection. mBio 2019; 10:e01440-19. [PMID: 31311883 PMCID: PMC6635531 DOI: 10.1128/mbio.01440-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022] Open
Abstract
Patient outcomes during infection are due to a complex interplay between the quality of medical care, host immunity factors, and the infecting pathogen's characteristics. To probe the influence of pathogen genotype on human survival, immune response, and other parameters of disease, we examined Cryptococcus neoformans isolates collected during the Cryptococcal Optimal Antiretroviral Therapy (ART) Timing (COAT) Trial in Uganda. We measured human participants' survival, meningitis disease parameters, immunologic phenotypes, and pathogen in vitro growth characteristics. We compared those clinical data to whole-genome sequences from 38 C. neoformans isolates of the most frequently observed sequence type (ST), ST93, in our Ugandan participant population and to sequences from an additional 18 strains of 9 other sequence types representing the known genetic diversity within the Ugandan Cryptococcus clinical isolates. We focused our analyses on 652 polymorphisms that were variable among the ST93 genomes, were not in centromeres or extreme telomeres, and were predicted to have a fitness effect. Logistic regression and principal component analysis identified 40 candidate Cryptococcus genes and 3 hypothetical RNAs associated with human survival, immunologic response, or clinical parameters. We infected mice with 17 available KN99α gene deletion strains for these candidate genes and found that 35% (6/17) directly influenced murine survival. Four of the six gene deletions that impacted murine survival were novel. Such bedside-to-bench translational research identifies important candidate genes for future studies on virulence-associated traits in human Cryptococcus infections.IMPORTANCE Even with the best available care, mortality rates in cryptococcal meningitis range from 20% to 60%. Disease is often due to infection by the fungus Cryptococcus neoformans and involves a complex interaction between the human host and the fungal pathogen. Although previous studies have suggested genetic differences in the pathogen impact human disease, it has proven quite difficult to identify the specific C. neoformans genes that impact the outcome of the human infection. Here, we take advantage of a Ugandan patient cohort infected with closely related C. neoformans strains to examine the role of pathogen genetic variants on several human disease characteristics. Using a pathogen whole-genome sequencing approach, we showed that 40 C. neoformans genes are associated with human disease. Surprisingly, many of these genes are specific to Cryptococcus and have unknown functions. We also show deletion of some of these genes alters disease in a mouse model of infection, confirming their role in disease. These findings are particularly important because they are the first to identify C. neoformans genes associated with human cryptococcal meningitis and lay the foundation for future studies that may lead to new treatment strategies aimed at reducing patient mortality.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katrina M Jackson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tami R McDonald
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yina Wang
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Benjamin D Lueck
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sara Bohjanen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kyle D Smith
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew Akampurira
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David B Meya
- Infectious Diseases Institute and School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - David R Boulware
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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11
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Bielska E, May RC. Extracellular vesicles of human pathogenic fungi. Curr Opin Microbiol 2019; 52:90-99. [PMID: 31280026 DOI: 10.1016/j.mib.2019.05.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/30/2019] [Indexed: 12/20/2022]
Abstract
Extracellular vesicles play a significant role in many aspects of cellular life including cell-to-cell communication, pathogenesis and cancer progression. However very little is known about their role in fungi and we are just at the beginning of understanding their influence on fungal pathophysiology and host-pathogen interactions. Recent findings have revealed a role for fungal vesicles in triggering anti-microbial activities as well as in modulating virulence strategies, suggesting potential new avenues for antifungal therapies. In this review, we summarize our current understanding of fungal extracellular vesicles, including their biogenesis, secretion and size variation, and discuss how they may influence the human immune response and some key questions that remain unanswered.
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Affiliation(s)
- Ewa Bielska
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Robin C May
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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12
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Wang ZA, Li LX, Doering TL. Unraveling synthesis of the cryptococcal cell wall and capsule. Glycobiology 2019; 28:719-730. [PMID: 29648596 DOI: 10.1093/glycob/cwy030] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 11/15/2022] Open
Abstract
Fungal pathogens cause devastating infections in millions of individuals each year, representing a huge but underappreciated burden on human health. One of these, the opportunistic fungus Cryptococcus neoformans, kills hundreds of thousands of patients annually, disproportionately affecting people in resource-limited areas. This yeast is distinguished from other pathogenic fungi by a polysaccharide capsule that is displayed on the cell surface. The capsule consists of two complex polysaccharide polymers: a mannan substituted with xylose and glucuronic acid, and a galactan with galactomannan side chains that bear variable amounts of glucuronic acid and xylose. The cell wall, with which the capsule is associated, is a matrix of alpha and beta glucans, chitin, chitosan, and mannoproteins. In this review, we focus on synthesis of the wall and capsule, both of which are critical for the ability of this microbe to cause disease and are distinct from structures found in either model yeasts or the mammals afflicted by this infection. Significant research effort over the last few decades has been applied to defining the synthetic machinery of these two structures, including nucleotide sugar metabolism and transport, glycosyltransferase activities, polysaccharide export, and assembly and association of structural elements. Discoveries in this area have elucidated fundamental biology and may lead to novel targets for antifungal therapy. In this review, we summarize the progress made in this challenging and fascinating area, and outline future research questions.
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Affiliation(s)
- Zhuo A Wang
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
| | - Lucy X Li
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO, USA
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13
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Liu YH, Deng HH, Li HN, Shi TF, Peng HP, Liu AL, Chen W, Hong GL. A DNA electrochemical biosensor based on homogeneous hybridization for the determination of Cryptococcus neoformans. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Bielska E, Sisquella MA, Aldeieg M, Birch C, O'Donoghue EJ, May RC. Pathogen-derived extracellular vesicles mediate virulence in the fatal human pathogen Cryptococcus gattii. Nat Commun 2018; 9:1556. [PMID: 29674675 PMCID: PMC5908794 DOI: 10.1038/s41467-018-03991-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/27/2018] [Indexed: 01/17/2023] Open
Abstract
The Pacific Northwest outbreak of cryptococcosis, caused by a near-clonal lineage of the fungal pathogen Cryptococcus gattii, represents the most significant cluster of life-threatening fungal infections in otherwise healthy human hosts currently known. The outbreak lineage has a remarkable ability to grow rapidly within human white blood cells, using a unique 'division of labour' mechanism within the pathogen population, where some cells adopt a dormant behaviour to support the growth of neighbouring cells. Here we demonstrate that pathogenic 'division of labour' can be triggered over large cellular distances and is mediated through the release of extracellular vesicles by the fungus. Isolated vesicles released by virulent strains are taken up by infected host macrophages and trafficked to the phagosome, where they trigger the rapid intracellular growth of non-outbreak fungal cells that would otherwise be eliminated by the host. Thus, long distance pathogen-to-pathogen communication via extracellular vesicles represents a novel mechanism to control complex virulence phenotypes in Cryptococcus gattii and, potentially, other infectious species.
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Affiliation(s)
- Ewa Bielska
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Marta Arch Sisquella
- Institut d' Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Crta de Can Ruti s/n, Badalona, 08916, Catalonia, Spain
| | - Maha Aldeieg
- School of Biological Sciences, University of Reading, Knight Building, Whiteknights Campus, Reading, RG6 6AJ, UK
| | - Charlotte Birch
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eloise J O'Donoghue
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Robin C May
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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15
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Gerstein AC, Nielsen K. It's not all about us: evolution and maintenance of Cryptococcus virulence requires selection outside the human host. Yeast 2017; 34:143-154. [PMID: 27862271 DOI: 10.1002/yea.3222] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/11/2022] Open
Abstract
Cryptococcus is predominantly an AIDS-related pathogen that causes significant morbidity and mortality in immunocompromised patients. Research studies have historically focused on understanding how the organism causes human disease through the use of in vivo and in vitro model systems to identify virulence factors. Cryptococcus is not an obligate pathogen, however, as human-human transmission is either absent or rare. Selection in the environment must thus be invoked to shape the evolution of this taxa, and directly influences genotypic and trait diversity. Importantly, the evolution and maintenance of pathogenicity must also stem directly from environmental selection. To that end, here we examine abiotic and biotic stresses in the environment, and discuss how they could shape the factors that are commonly identified as important virulence traits. We identify a number of important unanswered questions about Cryptococcus diversity and evolution that are critical for understanding this deadly pathogen, and discuss how implementation of modern sampling and genomic tools could be utilized to answer these questions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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16
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Abstract
Enzymes play key roles in fungal pathogenesis. Manipulation of enzyme expression or activity can significantly alter the infection process, and enzyme expression profiles can be a hallmark of disease. Hence, enzymes are worthy targets for better understanding pathogenesis and identifying new options for combatting fungal infections. Advances in genomics, proteomics, transcriptomics, and mass spectrometry have enabled the identification and characterization of new fungal enzymes. This review focuses on recent developments in the virulence-associated enzymes from Cryptococcus neoformans. The enzymatic suite of C. neoformans has evolved for environmental survival, but several of these enzymes play a dual role in colonizing the mammalian host. We also discuss new therapeutic and diagnostic strategies that could be based on the underlying enzymology.
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Longo LVG, Nakayasu ES, Pires JHS, Gazos-Lopes F, Vallejo MC, Sobreira TJP, Almeida IC, Puccia R. Characterization of Lipids and Proteins Associated to the Cell Wall of the Acapsular Mutant Cryptococcus neoformans Cap 67. J Eukaryot Microbiol 2015; 62:591-604. [PMID: 25733123 DOI: 10.1111/jeu.12213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 01/02/2023]
Abstract
Cryptococcus neoformans is an opportunistic human pathogen that causes life-threatening meningitis. In this fungus, the cell wall is exceptionally not the outermost structure due to the presence of a surrounding polysaccharide capsule, which has been highly studied. Considering that there is little information about C. neoformans cell wall composition, we aimed at describing proteins and lipids extractable from this organelle, using as model the acapsular mutant C. neoformans cap 67. Purified cell wall preparations were extracted with either chloroform/methanol or hot sodium dodecyl sulfate. Total lipids fractionated in silica gel 60 were analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS), while trypsin digested proteins were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). We detected 25 phospholipid species among phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, and phosphatidic acid. Two glycolipid species were identified as monohexosyl ceramides. We identified 192 noncovalently linked proteins belonging to different metabolic processes. Most proteins were classified as secretory, mainly via nonclassical mechanisms, suggesting a role for extracellular vesicles (EV) in transwall transportation. In concert with that, orthologs from 86% of these proteins have previously been reported both in fungal cell wall and/or in EV. The possible role of the presently described structures in fungal-host relationship is discussed.
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Affiliation(s)
- Larissa V G Longo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Ernesto S Nakayasu
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Jhon H S Pires
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Felipe Gazos-Lopes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Milene C Vallejo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Tiago J P Sobreira
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, 13083-970, São Paulo, Brazil
| | - Igor C Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
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18
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Peres da Silva R, Puccia R, Rodrigues ML, Oliveira DL, Joffe LS, César GV, Nimrichter L, Goldenberg S, Alves LR. Extracellular vesicle-mediated export of fungal RNA. Sci Rep 2015; 5:7763. [PMID: 25586039 PMCID: PMC5379013 DOI: 10.1038/srep07763] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/12/2014] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) play an important role in the biology of various organisms, including fungi, in which they are required for the trafficking of molecules across the cell wall. Fungal EVs contain a complex combination of macromolecules, including proteins, lipids and glycans. In this work, we aimed to describe and characterize RNA in EV preparations from the human pathogens Cryptococcus neoformans, Paracoccidiodes brasiliensis and Candida albicans, and from the model yeast Saccharomyces cerevisiae. The EV RNA content consisted mostly of molecules less than 250 nt long and the reads obtained aligned with intergenic and intronic regions or specific positions within the mRNA. We identified 114 ncRNAs, among them, six small nucleolar (snoRNA), two small nuclear (snRNA), two ribosomal (rRNA) and one transfer (tRNA) common to all the species considered, together with 20 sequences with features consistent with miRNAs. We also observed some copurified mRNAs, as suggested by reads covering entire transcripts, including those involved in vesicle-mediated transport and metabolic pathways. We characterized for the first time RNA molecules present in EVs produced by fungi. Our results suggest that RNA-containing vesicles may be determinant for various biological processes, including cell communication and pathogenesis.
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Affiliation(s)
- Roberta Peres da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia da Escola Paulista de Medicina-UNIFESP, São Paulo, SP, Brazil
| | - Marcio L Rodrigues
- 1] Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil [2] Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Débora L Oliveira
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luna S Joffe
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Gabriele V César
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
| | - Lysangela R Alves
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR, Curitiba, PR, Brazil
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