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Zhao H, Ju X, Nie Y, James TY, Liu XY. High-throughput screening carbon and nitrogen sources to promote growth and sporulation in Rhizopus arrhizus. AMB Express 2024; 14:76. [PMID: 38942930 PMCID: PMC11213844 DOI: 10.1186/s13568-024-01733-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-D-galactosamine and L-phenylalanine ranking at the top of the list. Eight substrates, especially L-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.
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Affiliation(s)
- Heng Zhao
- College of Life Sciences, Shandong Normal University, Jinan, 250358, China
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xiao Ju
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate School, China Pharmaceutical University, Nanjing, 211198, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, 243002, China
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, 250358, China.
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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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: 100] [Impact Index Per Article: 20.0] [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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Turner TL, Lane S, Jayakody LN, Zhang GC, Kim H, Cho W, Jin YS. Deletion of JEN1 and ADY2 reduces lactic acid yield from an engineered Saccharomyces cerevisiae, in xylose medium, expressing a heterologous lactate dehydrogenase. FEMS Yeast Res 2019; 19:5556531. [DOI: 10.1093/femsyr/foz050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/27/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Microorganisms have evolved to produce specific end products for many reasons, including maintaining redox balance between NAD+ and NADH. The yeast Saccharomyces cerevisiae, for example, produces ethanol as a primary end product from glucose for the regeneration of NAD+. Engineered S. cerevisiae strains have been developed to ferment lignocellulosic sugars, such as xylose, to produce lactic acid by expression of a heterologous lactate dehydrogenase (ldhA from Rhizopus oryzae) without genetic perturbation to the native ethanol pathway. Surprisingly, the engineered yeast strains predominantly produce ethanol from glucose, but produce lactic acid as the major product from xylose. Here, we provide initial evidence that the shift in product formation from ethanol to lactic acid during xylose fermentation is at least partially dependent on the presence of functioning monocarboxylate transporter genes/proteins, including JEN1 and ADY2, which are downregulated and unstable in the presence of glucose, but upregulated/stable on xylose. Future yeast metabolic engineering studies may find the feedstock/carbon selection, such as xylose, an important step toward improving the yield of target end products.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Lane
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lahiru N Jayakody
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Whiyeon Cho
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Abstract
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.
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Abe A, Oda Y, Asano K, Sone T. Rhizopus delemar is the proper name for Rhizopus oryzae fumaric-malic acid producers. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ayumi Abe
- Laboratory of Applied Microbiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Yuji Oda
- Department of Agricultural and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | | | - Teruo Sone
- Laboratory of Applied Microbiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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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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7
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Koutinas AA, Vlysidis A, Pleissner D, Kopsahelis N, Lopez Garcia I, Kookos IK, Papanikolaou S, Kwan TH, Lin CSK. Valorization of industrial waste and by-product streams via fermentation for the production of chemicals and biopolymers. Chem Soc Rev 2014; 43:2587-627. [DOI: 10.1039/c3cs60293a] [Citation(s) in RCA: 380] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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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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18
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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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Mertens JA, Burdick RC, Rooney AP. Identification, biochemical characterization, and evolution of the Rhizopus oryzae 99–880 polygalacturonase gene family. Fungal Genet Biol 2008; 45:1616-24. [DOI: 10.1016/j.fgb.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 09/22/2008] [Accepted: 09/30/2008] [Indexed: 11/25/2022]
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20
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Nagy V, Seidl V, Szakacs G, Komoń-Zelazowska M, Kubicek CP, Druzhinina IS. Application of DNA bar codes for screening of industrially important fungi: the haplotype of Trichoderma harzianum sensu stricto indicates superior chitinase formation. Appl Environ Microbiol 2007; 73:7048-58. [PMID: 17827332 PMCID: PMC2074977 DOI: 10.1128/aem.00995-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selection of suitable strains for biotechnological purposes is frequently a random process supported by high-throughput methods. Using chitinase production by Hypocrea lixii/Trichoderma harzianum as a model, we tested whether fungal strains with superior enzyme formation may be diagnosed by DNA bar codes. We analyzed sequences of two phylogenetic marker loci, internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA-encoding gene cluster and the large intron of the elongation factor 1-alpha gene, tef1, from 50 isolates of H. lixii/T. harzianum, which were also tested to determine their ability to produce chitinases in solid-state fermentation (SSF). Statistically supported superior chitinase production was obtained for strains carrying one of the observed ITS1 and ITS2 and tef1 alleles corresponding to an allele of T. harzianum type strain CBS 226.95. A tef1-based DNA bar code tool, TrichoCHIT, for rapid identification of these strains was developed. The geographic origin of the strains was irrelevant for chitinase production. The improved chitinase production by strains containing this haplotype was not due to better growth on N-acetyl-beta-D-glucosamine or glucosamine. Isoenzyme electrophoresis showed that neither the isoenzyme profile of N-acetyl-beta-glucosaminidases or the endochitinases nor the intensity of staining of individual chitinase bands correlated with total chitinase in the culture filtrate. The superior chitinase producers did not exhibit similarly increased cellulase formation. Biolog Phenotype MicroArray analysis identified lack of N-acetyl-beta-D-mannosamine utilization as a specific trait of strains with the chitinase-overproducing haplotype. This observation was used to develop a plate screening assay for rapid microbiological identification of the strains. The data illustrate that desired industrial properties may be an attribute of certain populations within a species, and screening procedures should thus include a balanced mixture of all genotypes of a given species.
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Affiliation(s)
- Viviana Nagy
- Department of Agricultural Chemical Technology, Technical University of Budapest, Gellert ter 4, 1111 Budapest, Hungary
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22
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Skory CD, Ibrahim AS. Native and modified lactate dehydrogenase expression in a fumaric acid producing isolate Rhizopus oryzae 99-880. Curr Genet 2007; 52:23-33. [PMID: 17551728 DOI: 10.1007/s00294-007-0135-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
Rhizopus oryzae is subdivided into two groups based on genetic and phenotypic differences. Type-I isolates accumulate primarily lactic acid when grown in the presence of a fermentable carbon source and contain two lactate dehydrogenase genes, ldhA and ldhB. Type-II isolates synthesize predominantly fumaric acid and only have an ldhB gene. In this study, we determined that ldhB transcript is only minimally expressed in the Type-II isolate R. oryzae 99-880. LdhB enzyme purified from gene clones isolated from the Type-I isolate R. oryzae NRRL 395 and the Type-II isolate R. oryzae 99-880 each showed reductive LDH activity (pyruvate to lactate), while no oxidative LDH activity (lactate to pyruvate) was detected in either preparation. A transformation system was then developed for the first time with R. oryzae 99-880, using a uracil auxotrophic isolate that could be complemented with an orotate phosphoribosyltransferase gene, pyrF, isolated in this study. Transformation of this Type-II isolate with the ldhA gene from R. oryzae NRRL 395 resulted in reductive LDH activity between 1.0 and 1.8 U/mg total protein. Additionally, transformed isolates grown with glucose accumulated up to 27 g lactic acid/l with a concurrent decrease in fumaric acid, ethanol, and glycerol compared with the untransformed and vector-transformed control strains.
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Affiliation(s)
- Christopher D Skory
- Bioproducts and Biocatalysis Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604, USA.
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Mertens JA, Skory CD. Isolation and Characterization of Two Genes That Encode Active Glucoamylase Without a Starch Binding Domain from Rhizopus oryzae. Curr Microbiol 2007; 54:462-6. [PMID: 17503147 DOI: 10.1007/s00284-006-0655-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2006] [Accepted: 03/09/2007] [Indexed: 11/29/2022]
Abstract
Glucoamylase obtained from Rhizopus sp. is frequently preferred for certain applications of starch modification or saccharification. The predominant enzyme, which contains a starch-binding domain on the amino terminus, has been previously characterized from several species. Additionally, the cDNA encoding this protein was cloned and found to show 100% identity to a R. oryzae strain 99-880 that has recently been sequenced by the Broad Institute of Harvard and Massachusetts Institute of Technology. Analysis of this genome indicates coding regions for two additional glucoamylase genes, amyC and amyD, lacking a starch-binding domain. The two genes encode proteins that are approximately 50% identical to the catalytic region of the AmyA protein and 67% identical to each other. The predicted AmyC and AmyD proteins contain the highly conserved signature sequences of Family 15 glycoside hydrolases. The two genes appear to be transcriptionally expressed in cultures grown in fermentable and gluconeogenic carbon sources. The predicted 49.7-kD AmyC and 48.8-kD AmyD proteins were expressed in several different ways using Pichia pastoris. When the sequence for putative secretion signal was left intact, glucoamylase activity was detected in the crude cell extracts, but no activity was present in the growth medium. However, replacement of this region with the yeast alpha-secretion signal resulted in secretion of active glucoamylase that was able to degrade soluble starch.
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Affiliation(s)
- Jeffrey A Mertens
- Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 North University Street, Peoria, IL 61604, USA.
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Mertens JA, Skory CD. Isolation and characterization of a second glucoamylase gene without a starch binding domain from Rhizopus oryzae. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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