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  • Springer  (160)
  • Public Library of Science  (22)
  • Blackwell Publishing Ltd  (15)
  • American Geophysical Union  (13)
  • Frontiers Media  (13)
  • 1
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeiner, C. A., Purvine, S. O., Zink, E., Wu, S., Pasa-Tolic, L., Chaput, D. L., Santelli, C. M., & Hansel, C. M. Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition. Frontiers in Microbiology, 12, (2021): 610497, https://doi.org/10.3389/fmicb.2021.610497.
    Description: Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.
    Description: This work was supported by the National Science Foundation, grant numbers EAR-1249489 and CBET-1336496, both awarded to CH, by a JGI-EMSL Collaborative Science Initiative grant (proposal number 48100) awarded to CH and CS, and by the University of St. Thomas. Personal support for CZ was also provided by Harvard University and by a Ford Foundation Predoctoral Fellowship administered by the National Academies. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory (grid.436923.9), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Biological and Environmental Research Program and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). Part of this research was performed at the Bauer Core Facility of the FAS Center for Systems Biology at Harvard University. A portion of the bioinformatics analysis was performed at Harvard’s FAS Research Computing facility.
    Keywords: Manganese oxides ; Filamentous fungi ; Geomicrobiology ; Proteomics ; Biomineralization ; Secretome
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Restoration ecology 3 (1995), S. 0 
    ISSN: 1526-100X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The effect of a pipeline corridor constructed through an ecological reserve in Southern California was investigated by assessing plant species composition and soil chemistry. A homogeneous plant community comprised primarily of exotic annuals was found along the entire length of the corridor. This community has low similarity to the adjacent native plant communities. Soil organic matter was significantly less on the disturbed corridor than in contiguous undisturbed areas. Both available nitrogen and extractable phosphorus values were greater in the disturbed corridor. By contrast, total nitrogen was significantly higher outside the pipeline. The more labile litter of the exotic annuals allows increased mineralization along the corridor than does the more recalcitrant litter of the native perennial shrubs in the undisturbed areas. Once established, the weedy exotic annual litter may completely turn over organic matter and nitrogen, favoring the persistence of the weedy annuals. These exotic annuals appear to be moving into three of the native communities - grassland, coastal sage, and oak woodland - that have less organic matter and a more open plant canopy. Poor restoration efforts can lead to the establishment of such exotics, subsequent invasion into the surrounding undisturbed habitat, and degradation of the reserve.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 544 (1988), S. 0 
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 540 (1988), S. 0 
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food safety 4 (1982), S. 0 
    ISSN: 1745-4565
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 41 (1976), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Characteristics are presented for Yersiniu enterocoliticu-like organisms isolated from vacuum-packaged beef and lamb stored for 21-35 days at l-3°C. Isolation of this organism was more frequent after 28 days of storage under vacuum conditions than under nonvacuum conditions (leaker packages). A higher incidence of isolates was obtained from cuts packaged under high vacuum conditions.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 53 (1988), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A comparison of three relatively rapid methods of determining free fatty acids concentrations in cheese was performed by correlating the results with a more laborious but accurate gas chromatographic (GC) technique. Acid Degree Values were found to correlate poorly with the GC data, particularly for short chain fatty acids. Values obtained using a Copper Soap Method correlated closely with the GC data for total and long chain fatty acids, but did not correlate as well with short chain fatty acids levels. The Extraction-Titration Method was found to be a simple and reliable technique that yielded values which correlate closely with short chain fatty acid concentrations.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 50 (1985), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A qualitative screening revealed the occurrence of lipase, esterase, protease, amylase, endo-1,4-β-D-glucanase, xylanase, pectinmethylesterase, polygalacturonase, catalase, β-D-glucosidase and β-D-galactosidase activities in the technical Aspergillus niger enzyme under study (Lipase 2212 D, Röhm). The isolation and purification of lipolytic activities were performed by combination of DEAE-Trisacryl M ion exchange chromatography, Sephadex G 50 gel filtration and hydrophobic chromatography using Phenylsepharose CL-4B. The individual purification steps were checked by specific enzyme visualization in ultrathin agar gels after ultrathin-layer isoelectric focusing (UIEF). Two UIEF homogeneous lipase isoenzymes (I and II) were isolated and characterized by the following parameters: isoelectric points (I: 4.0; II. 3.5); molecular weights (I: 31000 daltons; II: 19000 daltons); carbohydrate contents (I: 6%; II: 9%) and compositions; pH optima (I, II: 5-6); substrate specificities and various effectors.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 69 (2004), S. 0 
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: : In the past, deliberate contamination of foods in the U.S. has been committed by individual criminals, disgruntled employees, or political activists with a narrow agenda. After September 11, 2001, every nation has had to consider a much wider range of food security issues. Food is a global commodity and nearly every country both exports and imports foods. Every nation must consider the security of its domestic production and look beyond its borders to its trading partners to assure the safety of its food supply. In the nearly 2 years since September 11, 2001, many steps have been taken to improve food security. New legislation has been enacted to strengthen the ability of government to respond to terrorist threats. New relationships have been forged between food security agencies, law enforcement, and the intelligence community. Virtually every segment of the domestic and imported food supply has come under scrutiny in an effort to identify points of weakness and appropriate protective measures. Gaps in our knowledge about specific agents and food processes have been identified and research to fill these gaps has been initiated. This effort will continue for the foreseeable future and could have a wide range of benefits, including improvements to food safety, a reduction in product counterfeiting, and a reduction in the “gray market” food trade. The scale and diversity of the U.S. food supply makes it an attractive target, but at the same time makes it very resilient and responsive to emerging threats.
    Type of Medium: Electronic Resource
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