1
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Pairazamán OD, Woiciechowski AL, Zevallos LA, Tanobe VOA, Zandona A, Soccol CR. Fumaric acid production by Rhizopus species from acid hydrolysate of oil palm empty fruit bunches. Braz J Microbiol 2024; 55:1179-1187. [PMID: 38671219 PMCID: PMC11153437 DOI: 10.1007/s42770-024-01322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/23/2024] [Indexed: 04/28/2024] Open
Abstract
The hemicellulosic fraction of lignocellulosic biomass is a very important material, due to the significant concentration of pentoses present in its composition and that can be used sustainably in biotechnological processes such as the production of fumaric acid. Research efforts are currently being promoted for the proper disposal and valorization of empty fruit bunches (EFB) from oil palm. In this work, seventeen Rhizopus species were evaluated in a fermentation medium with EFB hydrolyzate, without detoxification, as a carbon source for fumaric acid production. Rhizopus circicans 1475 and Rhizopus 3271 achieved productions of 5.65 g.L-1 and 5.25 g.L-1 of fumaric acid at 30 °C, 120 rpm for 96 h, respectively. The percentage of consumed sugars, mainly pentoses, was 24.88% and 34.02% for R. circicans 1475 and R 3271, respectively. Soy peptone and ammonium sulfate were evaluated as nitrogen sources, where soy peptone stimulated the formation of biomass pellets while ammonium sulfate produced mycelia and clamps.
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Affiliation(s)
- Omar D Pairazamán
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
- Biological Science Department, National University of Cajamarca, Cajamarca, Peru
- Bacteriology Laboratory, Regional Public Health Laboratory, Cajamarca, Peru
| | - Adenise L Woiciechowski
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil.
- Chemical Engineering Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil.
| | - Luis A Zevallos
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
| | | | - Arion Zandona
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
- Chemical Engineering Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
| | - Carlos R Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
- Chemical Engineering Department, Federal University of Paraná, Brazil, Polytechnic Center, CP 19011, Curitiba, 81531-908, Brazil
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2
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Sjamsuridzal W, Khasanah M, Febriani R, Vebliza Y, Oetari A, Santoso I, Gandjar I. The effect of the use of commercial tempeh starter on the diversity of Rhizopus tempeh in Indonesia. Sci Rep 2021; 11:23932. [PMID: 34907227 PMCID: PMC8671487 DOI: 10.1038/s41598-021-03308-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
At present, only a single Rhizopus species, R. microsporus, can be found in fresh tempeh produced in Java, Indonesia. The loss of diversity of Rhizopus in tempeh has been associated with the widespread use of commercial tempeh starter in Indonesia since the 2000s. However, the identities of the previous Rhizopus strains associated with tempeh, which have been preserved in a culture collection in Indonesia, have not been verified. The present study aimed to verify the identities of 22 Rhizopus strains isolated from tempeh produced using the traditional tempeh starters from the 1960s to the 2000s. Phylogenetic analysis based on the ITS regions in the rRNA gene sequence data, revealed that the Rhizopus strains belonged to the species R. arrhizus (five strains); R. delemar (14 strains); and R. microsporus (three strains). Verification of the identities of these Rhizopus strains in the present study confirmed the loss of diversity of Rhizopus species in tempeh produced in Indonesia, particularly in Java. Our findings confirmed that the morphological changes in Rhizopus species isolated from tempeh as a result of centuries of domestication.
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Affiliation(s)
- Wellyzar Sjamsuridzal
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia. .,Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia.
| | - Mangunatun Khasanah
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
| | - Rela Febriani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
| | - Yura Vebliza
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
| | - Ariyanti Oetari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia.,Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
| | - Iman Santoso
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia.,Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
| | - Indrawati Gandjar
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, 16424, Indonesia
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3
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Tang Q, Huang J, Zhang S, Qin H, Dong Y, Wang C, Li D, Zhou R. Keystone microbes affect the evolution and ecological coexistence of the community via species/strain specificity. J Appl Microbiol 2021; 132:1227-1238. [PMID: 34427980 DOI: 10.1111/jam.15255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 02/02/2023]
Abstract
AIM Microbial communities exhibit different diversity and fluctuations in the ecological functions due to time and environmental migration. Despite a long history of research and a plethora of data, the factors determining the biodiversity and stability of ecosystems is still elusive. METHODS AND RESULTS Here, the Chinese Xiaoqu fermentation system was used as a template to explore the mechanism in which the species specificity and strain in the initial phase affect the community structure and metabolites in the subsequent micro-ecosystem. The micro-ecosystem has been applied for hundreds of years, and the main metabolic function can be reproduced and traced. CONCLUSIONS The result proved that Rhizopus spp. is a keystone microbe with a species/strain specificity affecting the trophic interaction niche and function of modules in the complex community through glucose. The fungal community was demonstrated to have a high sealing and stability, while the bacterial community was generally found to change the community structure, physiological function, and interaction relationship, producing strains with connector functions to adapt to fluctuations. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows that the taxonomic level of key microbial strains can be changed to affect the evolution of coexistence and functional realisation of the community.
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Affiliation(s)
- Qiuxiang Tang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Suyi Zhang
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Hui Qin
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Yi Dong
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Chao Wang
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Delin Li
- Luzhoulaojiao Company Limited, Luzhou, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,National Engineering Research Centre of Solid-State Brewing, Luzhou, China
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4
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Trabelsi H, Hadrich I, Neji S, Khemakhem N, Hammami B, Makni F, Sellami H, Ayadi A. Microsatellite analysis of the population structure in Rhizopus arrhizus. J Appl Microbiol 2020; 128:1793-1801. [PMID: 31965685 DOI: 10.1111/jam.14583] [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: 10/14/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Rhizopus arrhizus is recognized as an emergent agent of superficial and invasive mucormycosis. Despite an increasing number of these infections, the molecular epidemiology of Rhizopus species has not been well studied. MATERIALS AND METHODS In this study, 43 R. arrhizus strains (25 environmental and 18 clinical isolates) were genotyped using six novel panels of microsatellite markers. RESULTS Upon the analysis of 43 isolates, 4-8 distinct alleles were detected for each marker. The discriminatory power for the individual markers ranged from 0·522 to 0·830. The combination of all six markers yielded 33 different haplotypes with a high degree of discrimination (0·989 D value). A four-marker combination were selected as the most parsimonious panel achieving D > 0·95. One clinical isolate and one environmental isolate shared the same genotype suggesting the possible nosocomial outbreak of mucormycosis in hospitalized patients. We have noted that the strains isolated from cutaneous mucormycosis were different from the strains isolated from rhino-orbito-cerebral mucormycosis. Then, the hypothesis of particular tropism of infectious strains for a given site is not excluded. The standardized indices of association IA and rBarD were significantly different from zero (P < 0·01), suggesting a prevailing clonal reproduction. The environmental population was significantly differentiated from clinical populations (Fst = 0·2249). CONCLUSIONS Microsatellite typing method described in our study showed an excellent degree of discriminatory power. It is a promising tool for illuminating the molecular epidemiology of R. arrhizus species, including strain relatedness and transmission pathways.
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Affiliation(s)
- H Trabelsi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - I Hadrich
- Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - S Neji
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - N Khemakhem
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - B Hammami
- ENT Department, Habib Bourguiba Hospital, Sfax, Tunisia
| | - F Makni
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - H Sellami
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
| | - A Ayadi
- Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.,Fungi and Parasitic Molecular Biology Laboratory, School of Medicine, University of Sfax, Sfax, Tunisia
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5
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Walther G, Wagner L, Kurzai O. Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa. J Fungi (Basel) 2019; 5:E106. [PMID: 31739583 PMCID: PMC6958464 DOI: 10.3390/jof5040106] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera, Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed.
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Affiliation(s)
- Grit Walther
- German National Reference Center for Invasive Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, 07745 Jena, Germany; (L.W.); (O.K.)
| | - Lysett Wagner
- German National Reference Center for Invasive Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, 07745 Jena, Germany; (L.W.); (O.K.)
| | - Oliver Kurzai
- German National Reference Center for Invasive Fungal Infections, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, 07745 Jena, Germany; (L.W.); (O.K.)
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
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6
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An unusual cause of bowel obstruction: Rhizopus Arrhizus diverticulitis. Med Mycol Case Rep 2019; 25:15-18. [PMID: 31431881 PMCID: PMC6580311 DOI: 10.1016/j.mmcr.2019.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/24/2019] [Accepted: 06/07/2019] [Indexed: 11/23/2022] Open
Abstract
Mucormycosis is a fungal infection primarily afflicting immunocompromised or diabetic patients. Its presentation ranges from rhino-orbito-cerebral infections to disseminated mucormycosis with angioinvasion. We present a patient who developed a bowel obstruction one month after bone marrow transplant and was diagnosed with Rhizopus arrhizus diverticulitis despite antifungal therapy since transplantation. She underwent surgical removal with immediate fungal resurgence, declined further invasive intervention and was discharged on palliative isavuconazole. Seven months later she is alive with fungal containment.
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7
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Orikasa Y, Oda Y, Ohwada T. Identification of sucA, Encoding β-Fructofuranosidase, in Rhizopus microsporus. Microorganisms 2018; 6:E26. [PMID: 29534041 PMCID: PMC5874640 DOI: 10.3390/microorganisms6010026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 01/30/2023] Open
Abstract
Rhizopus microsporus NBRC 32995 was found to hydrolyze fructooligosaccharides (FOS), as well as sucrose, almost completely into monosaccharides through the production of sufficient amounts of organic acids, indicating that the complete hydrolysis of FOS was caused by the secretion of β-fructofuranosidase from fungal cells. Thus, the sucA gene, encoding a β-fructofuranosidase, was amplified by degenerate PCR, and its complete nucleotide sequence was determined. The total length of the sucA gene was 1590 bp, and the SucA protein of R. microsporus NBRC 32995 belonged to clade VIa, which also contains Rhizopus delemar and is closely related to Saccharomycotina, a subdivision of the Ascomycota.
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Affiliation(s)
- Yoshitake Orikasa
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
| | - Yuji Oda
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
| | - Takuji Ohwada
- Department of Life and Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
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8
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Odoni DI, Tamayo-Ramos JA, Sloothaak J, van Heck RGA, Martins Dos Santos VAP, de Graaff LH, Suarez-Diez M, Schaap PJ. Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation. PeerJ 2017; 5:e3133. [PMID: 28382234 PMCID: PMC5376114 DOI: 10.7717/peerj.3133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/01/2017] [Indexed: 11/20/2022] Open
Abstract
The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood. We set out to increase the knowledge about fumarate accumulation in R. delemar. To this end, we combined a transcriptomics and proteomics approach to identify key metabolic pathways involved in fumarate production in R. delemar, and propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Juan A Tamayo-Ramos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jasper Sloothaak
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ruben G A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.,LifeGlimmer GmBH, Berlin, Germany
| | - Leo H de Graaff
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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9
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Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM. An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun 2016; 7:12218. [PMID: 27447865 PMCID: PMC4961843 DOI: 10.1038/ncomms12218] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets.
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Affiliation(s)
- Marcus C. Chibucos
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sameh Soliman
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Teclegiorgis Gebremariam
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Hongkyu Lee
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Tracy H. Hazen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kizee A. Etienne
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David A. Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Shawn R. Lockhart
- Fungal Reference Laboratory, Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher D. Skory
- National Center for Agriculture Utilization Research, USDA, Agricultural Research Service, Peoria, Illinois 61604, USA
| | - Ashraf S. Ibrahim
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California 90502, USA
| | - Vincent M. Bruno
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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10
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11
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Xu Q, Liu Y, Li S, Jiang L, Huang H, Wen J. Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production. Bioprocess Biosyst Eng 2016; 39:1267-80. [DOI: 10.1007/s00449-016-1605-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/04/2016] [Indexed: 12/20/2022]
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12
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Papp T, Nyilasi I, Csernetics Á, Nagy G, Takó M, Vágvölgyi C. Improvement of Industrially Relevant Biological Activities in Mucoromycotina Fungi. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Differentiation of clinically relevant Mucorales Rhizopus microsporus and R. arrhizus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). J Med Microbiol 2015; 64:694-701. [DOI: 10.1099/jmm.0.000091] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Hartanti AT, Rahayu G, Hidayat I. Rhizopus Species from Fresh Tempeh Collected from Several Regions in Indonesia. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.1016/j.hjb.2015.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Piñar G, Sterflinger K, Pinzari F. Unmasking the measles-like parchment discoloration: molecular and microanalytical approach. Environ Microbiol 2015; 17:427-43. [PMID: 24684276 PMCID: PMC4371641 DOI: 10.1111/1462-2920.12471] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/20/2014] [Indexed: 12/03/2022]
Abstract
Many ancient parchments are defaced by red or purple maculae associated with localized destruction of collagen fibres. Although the main characteristics of this damage were present in most of the manuscripts analysed by many authors, no common microbial or fungal denominator has been found so far, and little or no correspondence between the microbial or fungal species isolated from materials could be addressed. In this study, culture-independent molecular methods and scanning electron microscopy (SEM) were used to identify fungal and bacterial communities on parchments affected by the purple stains. Protocols for c extraction and nucleic-acid-based strategies were selected for assays examining the community structure of fungi and bacteria on biodeteriorated parchment. Both SEM and molecular analysis detected the presence of bacterial and fungal cells in the damaged areas. Halophilic, halotolerant proteolytic bacterial species were selected by the saline environment provided by the parchment samples. As common microbial denominators, members of the Actinobacteria, mainly Saccharopolyspora spp. and species of Aspergillus, were detected in all investigated cases. It is proposed that a relationship exists between the phenomenon of purple spots on ancient parchments and that of the 'red heat' phenomenon, known to be present in some products manufactured with marine salt.
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Affiliation(s)
- Guadalupe Piñar
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Life SciencesMuthgasse 11, Vienna, 1190, Austria
| | - Katja Sterflinger
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Life SciencesMuthgasse 11, Vienna, 1190, Austria
| | - Flavia Pinzari
- ICRCPAL e Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario, Laboratorio di Biologia, Ministero per i Beni e le Attivita CulturaliRome, Italy
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Mendoza L, Vilela R, Voelz K, Ibrahim AS, Voigt K, Lee SC. Human Fungal Pathogens of Mucorales and Entomophthorales. Cold Spring Harb Perspect Med 2014; 5:cshperspect.a019562. [PMID: 25377138 DOI: 10.1101/cshperspect.a019562] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In recent years, we have seen an increase in the number of immunocompromised cohorts as a result of infections and/or medical conditions, which has resulted in an increased incidence of fungal infections. Although rare, the incidence of infections caused by fungi belonging to basal fungal lineages is also continuously increasing. Basal fungal lineages diverged at an early point during the evolution of the fungal lineage, in which, in a simplified four-phylum fungal kingdom, Zygomycota and Chytridiomycota belong to the basal fungi, distinguishing them from Ascomycota and Basidiomycota. Currently there are no known human infections caused by fungi in Chytridiomycota; only Zygomycotan fungi are known to infect humans. Hence, infections caused by zygomycetes have been called zygomycosis, and the term "zygomycosis" is often used as a synonym for "mucormycosis." In the four-phylum fungal kingdom system, Zygomycota is classified mainly based on morphology, including the ability to form coenocytic (aseptated) hyphae and zygospores (sexual spores). In the Zygomycota, there are 10 known orders, two of which, the Mucorales and Entomophthorales, contain species that can infect humans, and the infection has historically been known as zygomycosis. However, recent multilocus sequence typing analyses (the fungal tree of life [AFTOL] project) revealed that the Zygomycota forms not a monophyletic clade but instead a polyphyletic clade, whereas Ascomycota and Basidiomycota are monophyletic. Thus, the term "zygomycosis" needed to be further specified, resulting in the terms "mucormycosis" and "entomophthoramycosis." This review covers these two different types of fungal infections.
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Affiliation(s)
- Leonel Mendoza
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48424-1031 Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, Michigan 48424-1031
| | - Raquel Vilela
- Biomedical Laboratory Diagnostics, Michigan State University, East Lansing, Michigan 48424-1031 Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Minas Gerais, CEP33400000 Belo Horizonte, Brazil Belo Horizonte Brazil; Superior Institute of Medicine (ISMD), Minas Gerais, CEP33400000 Belo Horizonte, Brazil
| | - Kerstin Voelz
- Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom The National Institute of Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom B15 2WB
| | - Ashraf S Ibrahim
- Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, St. John's Cardiovascular Research Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502 David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology and University of Jena, Faculty of Biology and Pharmacy, Institute of Microbiology, Neugasse 25, 07743 Jena, Germany
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
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Dolatabadi S, de Hoog GS, Meis JF, Walther G. Species boundaries and nomenclature ofRhizopus arrhizus(syn.R. oryzae). Mycoses 2014; 57 Suppl 3:108-27. [DOI: 10.1111/myc.12228] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Somayeh Dolatabadi
- CBS-KNAW Fungal Biodiversity Centre; Utrecht the Netherland
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam the Netherlands
| | - G. Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre; Utrecht the Netherland
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam the Netherlands
- Peking University Health Science Center; Research Center for Medical Mycology; Beijing China
- Sun Yat-sen Memorial Hospital; Sun Yat-sen University; Guangzhou China
- Shanghai Institute of Medical Mycology; Changzheng Hospital; Second Military Medical University; Shanghai China. Basic Pathology Department; Federal University of Paraná State; Curitiba Paraná Brazil
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases; Canisius-Wilhelmina Hospital; Nijmegen the Netherlands
- Department of Medical Microbiology; Radboud University Medical Centre; Nijmegen the Netherlands
| | - Grit Walther
- Institute of Microbiology; Department of Microbiology and Molecular Biology; University of Jena; Jena Germany
- Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute; Jena Microbial Resource Collection; Jena Germany
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High levels of malic acid production by the bioconversion of corn straw hydrolyte using an isolated Rhizopus delemar strain. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0047-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Isavuconazole therapy protects immunosuppressed mice from mucormycosis. Antimicrob Agents Chemother 2014; 58:2450-3. [PMID: 24492363 DOI: 10.1128/aac.02301-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the in vitro and in vivo efficacies of the investigational drug isavuconazole against mucormycosis due to Rhizopus delemar. Isavuconazole was effective, with MIC and minimal fungicidal concentration (MFC) values ranging between 0.125 and 1.00 μg/ml. A high dose of isavuconazole prolonged the survival time and lowered the tissue fungal burden of cyclophosphamide/cortisone acetate-treated mice infected with R. delemar and was as effective as a high-dose liposomal amphotericin B treatment. These results support the further development of this azole against mucormycosis.
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Agunbiade TA, Sun W, Coates BS, Djouaka R, Tamò M, Ba MN, Binso-Dabire C, Baoua I, Olds BP, Pittendrigh BR. Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PLoS One 2013; 8:e79929. [PMID: 24278221 PMCID: PMC3838393 DOI: 10.1371/journal.pone.0079929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, Anoplocnemis curvipes Fabricius (Hemiptera: Coreidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, Aphis craccivora Koch (Hemiptera: Aphididae) and flower thrips, Megalurothrips sjostedti Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. The reads were de novo assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, Buchnera aphidicola, were identified among A. craccivora transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa.
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Affiliation(s)
- Tolulope A. Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | | | - Manuele Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - Malick N. Ba
- Institut de l’Environnement et de Recherches Agricoles, Ouagadougou, Burkina Faso
| | | | - Ibrahim Baoua
- Institut National de la Recherche Agronomique du Niger, Maradi, Niger
| | - Brett P. Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Walther G, Pawłowska J, Alastruey-Izquierdo A, Wrzosek M, Rodriguez-Tudela J, Dolatabadi S, Chakrabarti A, de Hoog G. DNA barcoding in Mucorales: an inventory of biodiversity. PERSOONIA 2013; 30:11-47. [PMID: 24027345 PMCID: PMC3734965 DOI: 10.3767/003158513x665070] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/01/2013] [Indexed: 11/25/2022]
Abstract
The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.
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Affiliation(s)
- G. Walther
- Institute of Microbiology, Department of Microbiology and Molecular Biology, University of Jena, Jena, Germany
- Leibniz-Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena Microbial Resource Collection, Jena, Germany
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - J. Pawłowska
- Department of Systematics and Plant Geography, University of Warsaw, Warsaw, Poland
| | - A. Alastruey-Izquierdo
- Instituto de Salud Carlos III Mycology Department, Spanish National Center for Microbiology, Madrid, Spain
| | - M. Wrzosek
- Department of Systematics and Plant Geography, University of Warsaw, Warsaw, Poland
| | - J.L. Rodriguez-Tudela
- Instituto de Salud Carlos III Mycology Department, Spanish National Center for Microbiology, Madrid, Spain
| | - S. Dolatabadi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - A. Chakrabarti
- Departments of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - G.S. de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Peking University Health Science Center, Research Center for Medical Mycology, Beijing, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Ferreira JA, Lennartsson PR, Edebo L, Taherzadeh MJ. Zygomycetes-based biorefinery: present status and future prospects. BIORESOURCE TECHNOLOGY 2013; 135:523-532. [PMID: 23127833 DOI: 10.1016/j.biortech.2012.09.064] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 06/01/2023]
Abstract
Fungi of the phylum Zygomycetes fulfil all requirements for being utilized as core catalysts in biorefineries, and would be useful in creating new sustainable products. Apart from the extended use of Zygomycetes in preparing fermented foods, industrial metabolites such as lactic acid, fumaric acid, and ethanol are produced from a vast array of feedstocks with the aid of Zygomycetes. These fungi produce enzymes that facilitate their assimilation of various complex substrates, e.g., starch, cellulose, phytic acid, and proteins, which is relevant from an industrial point of view. The enzymes produced are capable of catalyzing various reactions involved in biodiesel production, preparation of corticosteroid drugs, etc. Biomass produced with the aid of Zygomycetes consists of proteins with superior amino acid composition, but also lipids and chitosan. The biomass is presently being tested for animal feed purposes, such as fish feed, as well as for lipid extraction and chitosan production. Complete or partial employment of Zygomycetes in biorefining procedures is consequently attractive, and is expected to be implemented within a near future.
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Affiliation(s)
- Jorge A Ferreira
- School of Engineering, University of Borås, SE 501 90 Borås, Sweden
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Abstract
This article surveys methods for the enzymatic conversion of starch, involving hydrolases and nonhydrolyzing enzymes, as well as the role of microorganisms producing such enzymes. The sources of the most common enzymes are listed. These starch conversions are also presented in relation to their applications in the food, pharmaceutical, pulp, textile, and other branches of industry. Some sections are devoted to the fermentation of starch to ethanol and other products, and to the production of cyclodextrins, along with the properties of these products. Light is also shed on the enzymes involved in the digestion of starch in human and animal organisms. Enzymatic processes acting on starch are useful in structural studies of the substrates and in understanding the characteristics of digesting enzymes. One section presents the application of enzymes to these problems. The information that is included covers the period from the early 19th century up to 2009.
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The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies. Persoonia - Molecular Phylogeny and Evolution of Fungi 2013; 30:57-76. [PMID: 24027347 PMCID: PMC3734967 DOI: 10.3767/003158513x666259] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 01/01/2013] [Indexed: 02/01/2023]
Abstract
The Mucorales (Mucoromycotina) are one of the most ancient groups of fungi comprising ubiquitous, mostly saprotrophic organisms. The first comprehensive molecular studies 11 yr ago revealed the traditional classification scheme, mainly based on morphology, as highly artificial. Since then only single clades have been investigated in detail but a robust classification of the higher levels based on DNA data has not been published yet. Therefore we provide a classification based on a phylogenetic analysis of four molecular markers including the large and the small subunit of the ribosomal DNA, the partial actin gene and the partial gene for the translation elongation factor 1-alpha. The dataset comprises 201 isolates in 103 species and represents about one half of the currently accepted species in this order. Previous family concepts are reviewed and the family structure inferred from the multilocus phylogeny is introduced and discussed. Main differences between the current classification and preceding concepts affects the existing families Lichtheimiaceae and Cunninghamellaceae, as well as the genera Backusella and Lentamyces which recently obtained the status of families along with the Rhizopodaceae comprising Rhizopus, Sporodiniella and Syzygites. Compensatory base change analyses in the Lichtheimiaceae confirmed the lower level classification of Lichtheimia and Rhizomucor while genera such as Circinella or Syncephalastrum completely lacked compensatory base changes.
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Zhang B, Yang ST. Metabolic engineering of Rhizopus oryzae: Effects of overexpressing fumR gene on cell growth and fumaric acid biosynthesis from glucose. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Orikasa Y, Oda Y. Molecular characterization of β-fructofuranosidases from Rhizopus delemar and Amylomyces rouxii. Folia Microbiol (Praha) 2012. [DOI: 10.1007/s12223-012-0211-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Key technologies for the industrial production of fumaric acid by fermentation. Biotechnol Adv 2012; 30:1685-96. [DOI: 10.1016/j.biotechadv.2012.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 08/02/2012] [Accepted: 08/15/2012] [Indexed: 11/22/2022]
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Production of lactic acid from xylose and wheat straw by Rhizopus oryzae. J Biosci Bioeng 2012; 114:166-9. [DOI: 10.1016/j.jbiosc.2012.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/08/2012] [Accepted: 03/26/2012] [Indexed: 11/19/2022]
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Zhang B, Skory CD, Yang ST. Metabolic engineering of Rhizopus oryzae: effects of overexpressing pyc and pepc genes on fumaric acid biosynthesis from glucose. Metab Eng 2012; 14:512-20. [PMID: 22814110 DOI: 10.1016/j.ymben.2012.07.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/20/2012] [Accepted: 07/06/2012] [Indexed: 12/25/2022]
Abstract
Fumaric acid, a dicarboxylic acid used as a food acidulant and in manufacturing synthetic resins, can be produced from glucose in fermentation by Rhizopus oryzae. However, the fumaric acid yield is limited by the co-production of ethanol and other byproducts. To increase fumaric acid production, overexpressing endogenous pyruvate carboxylase (PYC) and exogenous phosphoenolpyruvate carboxylase (PEPC) to increase the carbon flux toward oxaloacetate were investigated. Compared to the wild type, the PYC activity in the pyc transformants increased 56%-83%, whereas pepc transformants exhibited significant PEPC activity (3-6 mU/mg) that was absent in the wild type. Fumaric acid production by the pepc transformant increased 26% (0.78 g/g glucose vs. 0.62 g/g for the wild type). However, the pyc transformants grew poorly and had low fumaric acid yields (<0.05 g/g glucose) due to the formation of large cell pellets that limited oxygen supply and resulted in the accumulation of ethanol with a high yield of 0.13-0.36 g/g glucose. This study is the first attempt to use metabolic engineering to modify the fumaric acid biosynthesis pathway to increase fumaric acid production in R. oryzae.
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Affiliation(s)
- Baohua Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH 43210, USA
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Meussen BJ, de Graaff LH, Sanders JPM, Weusthuis RA. Metabolic engineering of Rhizopus oryzae for the production of platform chemicals. Appl Microbiol Biotechnol 2012; 94:875-86. [PMID: 22526790 PMCID: PMC3339055 DOI: 10.1007/s00253-012-4033-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 11/28/2022]
Abstract
Rhizopus oryzae is a filamentous fungus belonging to the Zygomycetes. It is among others known for its ability to produce the sustainable platform chemicals L: -(+)-lactic acid, fumaric acid, and ethanol. During glycolysis, all fermentable carbon sources are metabolized to pyruvate and subsequently distributed over the pathways leading to the formation of these products. These platform chemicals are produced in high yields on a wide range of carbon sources. The yields are in excess of 85 % of the theoretical yield for L: -(+)-lactic acid and ethanol and over 65 % for fumaric acid. The study and optimization of the metabolic pathways involved in the production of these compounds requires well-developed metabolic engineering tools and knowledge of the genetic makeup of this organism. This review focuses on the current metabolic engineering techniques available for R. oryzae and their application on the metabolic pathways of the main fermentation products.
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Affiliation(s)
- Bas J Meussen
- Fungal Systems Biology, Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
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Abstract
Fermentative fumaric acid production from renewable resources may become competitive with petrochemical production. This will require very efficient processes. So far, using Rhizopus strains, the best fermentations reported have achieved a fumaric acid titer of 126 g/L with a productivity of 1.38 g L(-1) h(-1) and a yield on glucose of 0.97 g/g. This requires pH control, aeration, and carbonate/CO(2) supply. Limitations of the used strains are their pH tolerance, morphology, accessibility for genetic engineering, and partly, versatility to alternative carbon sources. Understanding of the mechanism and energetics of fumaric acid export by Rhizopus strains will be a success factor for metabolic engineering of other hosts for fumaric acid production. So far, metabolic engineering has been described for Escherichia coli and Saccharomyces cerevisiae.
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Affiliation(s)
- Adrie J J Straathof
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands,
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Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, Bonito G, Porter TM, Anishchenko IM, Heitman J, Vilgalys R. Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. PLoS One 2010; 5:e15273. [PMID: 21151560 PMCID: PMC3000332 DOI: 10.1371/journal.pone.0015273] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 11/04/2010] [Indexed: 01/07/2023] Open
Abstract
The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/-) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (-) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.
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Affiliation(s)
- Andrii P Gryganskyi
- Department of Biology, Duke University, Durham, North Carolina, United States of America.
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Skory CD, Hector RE, Gorsich SW, Rich JO. Analysis of a functional lactate permease in the fungus Rhizopus. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Dannaoui E. Molecular tools for identification of Zygomycetes and the diagnosis of zygomycosis. Clin Microbiol Infect 2009; 15 Suppl 5:66-70. [PMID: 19754761 DOI: 10.1111/j.1469-0691.2009.02983.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of Zygomycetes and diagnosis of zygomycosis are notoriously difficult. However, there have been recent advances, particularly in the availability and evaluation of new molecular approaches. Two main issues are of importance: the identification to species level of a strain isolated in culture, and the identification of a zygomycete in tissues. By using several molecular targets and by increasing the number of available DNA sequences in international databases, several studies have shown that accurate molecular identification of Zygomycetes to species level is feasible. The internal transcribed spacer (ITS) region may be used as a first-line molecular target for the identification of Zygomycetes in pure culture. However, cultures from infected tissues are often negative and the different Zygomycetes share similar morphology according to histopathology. Furthermore, differentiation of a zygomycete from another hyalohyphomycete can sometimes be difficult in histopathology. Thus, alternative methods for the diagnosis of zygomycosis and for species identification directly from tissues are needed. For this purpose, molecular methods have been recently evaluated, both on unfixed fresh/frozen material and on formalin-fixed, paraffin-embedded biopsies. This review discusses the molecular approaches currently available for the identification of Zygomycetes and the diagnosis of zygomycosis.
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Affiliation(s)
- E Dannaoui
- Centre National de Référence Mycologie et Antifongiques, Unité de Mycologie Moléculaire, CNRS URA3012, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
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Identification and characterization of Rhizot, a novel LTR retrotransposon of Rhizopus oryzae and R. delemar. Biosci Biotechnol Biochem 2009; 73:1860-2. [PMID: 19661716 DOI: 10.1271/bbb.90017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A novel retrotransposon Rhizot was identified in Rhizopus oryzae and R. delemar. Rhizot has a unique structure that consists of a pol ORF similar to non-LTR (long terminal repeat) retorotransposons between two LTRs. Rhizot was distributed in all Rhizopus species tested. The Rhizot pol gene was transcribed in the liquid culture, and was induced by UV and oxidative stress.
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Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 2009; 5:e1000549. [PMID: 19578406 PMCID: PMC2699053 DOI: 10.1371/journal.pgen.1000549] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 06/04/2009] [Indexed: 01/12/2023] Open
Abstract
Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called “zygomycetes,” R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99–880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin–proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14α-demethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments. Rhizopus oryzae is a widely dispersed fungus that can cause fatal infections in people with suppressed immune systems, especially diabetics or organ transplant recipients. Antibiotic therapy alone is rarely curative, particularly in patients with disseminated infection. We sequenced the genome of a pathogenic R. oryzae strain and found evidence that the entire genome had been duplicated at some point in its evolution and retained two copies of three extremely sophisticated systems involved in energy generation and utilization. The ancient whole-genome duplication, together with recent gene duplications, has led to the expansion of gene families related to pathogen virulence, fungal-specific cell wall synthesis, and signal transduction, which may contribute to the aggressive and frequently life-threatening growth of this organism. We also identified cell wall synthesis enzymes, essential for fungal cell integrity but absent in mammals, which may present potential targets for developing novel diagnostic and therapeutic treatments. R. oryzae represents the first sequenced fungus from the early lineages of the fungal phylogenetic tree, and thus the genome sequence sheds light on the evolution of the entire fungal kingdom.
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Sequence-based identification of Aspergillus, fusarium, and mucorales species in the clinical mycology laboratory: where are we and where should we go from here? J Clin Microbiol 2008; 47:877-84. [PMID: 19073865 DOI: 10.1128/jcm.01685-08] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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