Special Issue "Filamentous Fungi in White Biotechnology"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 September 2017)

Special Issue Editors

Guest Editor
Prof. Annele Hatakka

Department of Food and Environmental Sciences Faculty of Agriculture and Forestry, University of Helsinki, Finland
Website | E-Mail
Interests: white-rot fungi; lignin and cellulose biodegradation; enzymes; biotechnology in the pulp and paper industry; mycoremediation
Guest Editor
Dr. Taina Lundell

Department of Food and Environmental Sciences Faculty of Agriculture and Forestry, University of Helsinki, Finland
Website | E-Mail
Interests: Basidiomycota; wood decay fungi; fungal genomics and evolution; fungal biotechnology; ecophysiology of forest fungi; enzymes; lignocellulose biodegradation

Special Issue Information

Dear Colleagues,

White biotechnology, also known as industrial biotechnology, uses enzymes and micro-organisms to make biobased products in sectors such as chemicals, food and feed, detergents, paper and pulp, textiles, and bioenergy. In doing so, it uses renewable raw materials and is one of the most promising, innovative approaches towards lowering greenhouse gas emissions (http://www.europabio.org/industrial-biotech). White biotechnology also employs living organisms as cell factories preferably utilizing renewable natural resources such as lignocellulose for production of a variety of materials and bio-compounds with energy efficiency, increased productivity and environmentally sustainable characteristics. Filamentous fungi are a huge resource of different enzymes and bioactive metabolites, and form a “hidden treasure” for future use in biotechnological applications. Moreover, recent approaches in fungal genomics are opening a plethora of yet unknown enzyme activities, genes and metabolic pathways.

This Special Issue will publish papers focusing on selected aspects of the topics above introduced, with particular interests towards: (i) genomics of taxonomically diverse Basidiomycota and Ascomycota as sources of novel activities, such as the divergent oxidoreductases involved in decomposition of plant biomasses; (ii) filamentous fungi as industrial and experimental hosts for production of enzymes and added-value compounds; (iii) fungi as bioconversion agents in utilization of waste feedstocks, and (iv) future prospects on systems biology of filamentous fungi and their enzymes in synthetic biology. We emphasize studies dealing with genome data mining, metabolomics and transcriptomics, to enzyme functionality, to develop processes for biofuels, bioenergy and biorefining of plant biomasses.

Prof. Annele Hatakka
Dr. Taina Lundell
Guest Editors

Manuscript Submission Information

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Keywords

  • filamentous fungi
  • ascomycetes
  • basidiomycetes
  • fungal genomics
  • transcriptomics
  • metabolomics
  • oxidoreductases
  • synthetic biology
  • bioenergy and biofuels
  • biorefining of lignocellulose biomass

Published Papers (8 papers)

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Open AccessArticle Enzymatic Preparation of 2,5-Furandicarboxylic Acid (FDCA)—A Substitute of Terephthalic Acid—By the Joined Action of Three Fungal Enzymes
Microorganisms 2018, 6(1), 5; https://doi.org/10.3390/microorganisms6010005
Received: 6 December 2017 / Revised: 5 January 2018 / Accepted: 6 January 2018 / Published: 9 January 2018
Cited by 6 | PDF Full-text (3501 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different [...] Read more.
Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different reaction steps was evaluated and apparent kinetic data (Michaelis-Menten constants, turnover numbers, specific constants) were calculated for different enzyme-substrate ratios and enzyme combinations. Finally, the target product, 2,5-furandicarboxylic acid (FDCA), was prepared in a multi-enzyme cascade reaction combining three fungal oxidoreductases at micro-scale. Furthermore, an oxidase-like reaction is proposed for heme-containing peroxidases, such as UPO, horseradish peroxidase, or catalase, causing the conversion of 5-formyl-2-furancarboxylic acid into FDCA in the absence of exogenous hydrogen peroxide. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Pichia pastoris is a Suitable Host for the Heterologous Expression of Predicted Class I and Class II Hydrophobins for Discovery, Study, and Application in Biotechnology
Microorganisms 2018, 6(1), 3; https://doi.org/10.3390/microorganisms6010003
Received: 13 November 2017 / Revised: 15 December 2017 / Accepted: 29 December 2017 / Published: 5 January 2018
Cited by 2 | PDF Full-text (3554 KB) | HTML Full-text | XML Full-text
Abstract
The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing [...] Read more.
The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing systems for their heterologous expression challenging. In this article, we describe the development of Pichia pastoris KM71H strains capable of solubly producing the full set of predicted Cordyceps militaris hydrophobins CMil1 (Class IA), CMil2 (Class II), and CMil3 (IM) at mg/L yields with the use of 6His-tags not only for purification but for their detection. This result further demonstrates the feasibility of using P. pastoris as a host organism for the production of hydrophobins from all Ascomycota Class I subdivisions (a classification our previous work defined) as well as Class II. We highlight the specific challenges related to the production of hydrophobins, notably the challenge in detecting the protein that will be described, in particular during the screening of transformants. Together with the literature, our results continue to show that P. pastoris is a suitable host for the soluble heterologous expression of hydrophobins with a wide range of properties. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Physiological Peculiarities of Lignin-Modifying Enzyme Production by the White-Rot Basidiomycete Coriolopsis gallica Strain BCC 142
Microorganisms 2017, 5(4), 73; https://doi.org/10.3390/microorganisms5040073
Received: 19 September 2017 / Revised: 9 November 2017 / Accepted: 16 November 2017 / Published: 17 November 2017
Cited by 5 | PDF Full-text (881 KB) | HTML Full-text | XML Full-text
Abstract
Sixteen white-rot Basidiomycota isolates were screened for production of lignin-modifying enzymes (LME) in glycerol- and mandarin peel-containing media. In the synthetic medium, Cerrena unicolor strains were the only high laccase (Lac) (3.2–9.4 U/mL) and manganese peroxidase (MnP) (0.56–1.64 U/mL) producers while one isolate [...] Read more.
Sixteen white-rot Basidiomycota isolates were screened for production of lignin-modifying enzymes (LME) in glycerol- and mandarin peel-containing media. In the synthetic medium, Cerrena unicolor strains were the only high laccase (Lac) (3.2–9.4 U/mL) and manganese peroxidase (MnP) (0.56–1.64 U/mL) producers while one isolate Coriolopsis gallica was the only lignin peroxidase (LiP) (0.07 U/mL) producer. Addition of mandarin peels to the synthetic medium promoted Lac production either due to an increase in fungal biomass (Funalia trogii, Trametes hirsuta, and T. versicolor) or enhancement of enzyme production (C. unicolor, Merulius tremellosus, Phlebia radiata, Trametes ochracea). Mandarin peels favored enhanced MnP and LiP secretion by the majority of the tested fungi. The ability of LiP activity production by C. gallica, C. unicolor, F. trogii, T. ochracea, and T. zonatus in the medium containing mandarin-peels was reported for the first time. Several factors, such as supplementation of the nutrient medium with a variety of lignocellulosic materials, nitrogen source or surfactant (Tween 80, Triton X-100) significantly influenced production of LME by a novel strain of C. gallica. Moreover, C. gallica was found to be a promising LME producer with a potential for an easy scale up cultivation in a bioreactor and high enzyme yields (Lac-9.4 U/mL, MnP-0.31 U/mL, LiP-0.45 U/mL). Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle A Two-Step Bioconversion Process for Canolol Production from Rapeseed Meal Combining an Aspergillus niger Feruloyl Esterase and the Fungus Neolentinus lepideus
Microorganisms 2017, 5(4), 67; https://doi.org/10.3390/microorganisms5040067
Received: 5 September 2017 / Revised: 2 October 2017 / Accepted: 11 October 2017 / Published: 14 October 2017
Cited by 1 | PDF Full-text (1866 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rapeseed meal is a cheap and abundant raw material, particularly rich in phenolic compounds of biotechnological interest. In this study, we developed a two-step bioconversion process of naturally occurring sinapic acid (4-hydroxy-3,5-dimethoxycinnamic acid) from rapeseed meal into canolol by combining the complementary potentialities [...] Read more.
Rapeseed meal is a cheap and abundant raw material, particularly rich in phenolic compounds of biotechnological interest. In this study, we developed a two-step bioconversion process of naturally occurring sinapic acid (4-hydroxy-3,5-dimethoxycinnamic acid) from rapeseed meal into canolol by combining the complementary potentialities of two filamentous fungi, the micromycete Aspergillus niger and the basidiomycete Neolentinus lepideus. Canolol could display numerous industrial applications because of its high antioxidant, antimutagenic and anticarcinogenic properties. In the first step of the process, the use of the enzyme feruloyl esterase type-A (named AnFaeA) produced with the recombinant strain A. niger BRFM451 made it possible to release free sinapic acid from the raw meal by hydrolysing the conjugated forms of sinapic acid in the meal (mainly sinapine and glucopyranosyl sinapate). An amount of 39 nkat AnFaeA per gram of raw meal, at 55 °C and pH 5, led to the recovery of 6.6 to 7.4 mg of free sinapic acid per gram raw meal, which corresponded to a global hydrolysis yield of 68 to 76% and a 100% hydrolysis of sinapine. Then, the XAD2 adsorbent (a styrene and divinylbenzene copolymer resin), used at pH 4, enabled the efficient recovery of the released sinapic acid, and its concentration after elution with ethanol. In the second step, 3-day-old submerged cultures of the strain N. lepideus BRFM15 were supplied with the recovered sinapic acid as the substrate of bioconversion into canolol by a non-oxidative decarboxylation pathway. Canolol production reached 1.3 g/L with a molar yield of bioconversion of 80% and a productivity of 100 mg/L day. The same XAD2 resin, when used at pH 7, allowed the recovery and purification of canolol from the culture broth of N. lepideus. The two-step process used mild conditions compatible with green chemistry. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Melanisation of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture?
Microorganisms 2017, 5(2), 22; https://doi.org/10.3390/microorganisms5020022
Received: 17 March 2017 / Revised: 13 April 2017 / Accepted: 28 April 2017 / Published: 4 May 2017
Cited by 3 | PDF Full-text (973 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus [...] Read more.
Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus spp. In Aspergillus terreus, the pigmentation has remained mysterious with only one class of melanin biogenesis being found. In this study, we examined an intriguing, partially annotated gene cluster of A. terreus strain NIH2624, utilizing previously sequenced transcriptome and improved gene expression data of strain MUCL 38669, under the influence of a suggested quorum sensing inducing metabolite, butyrolactone I. The core polyketide synthase (PKS) gene of the cluster was predicted to be significantly longer on the basis of the obtained transcriptional data, and the surrounding cluster was positively regulated by butyrolactone I at the late growth phase of submerged culture, presumably during sporulation. Phylogenetic analysis of the extended PKS revealed remarkable similarity with a group of known pigments of Fusarium spp., indicating a similar function for this PKS. We present a hypothesis of this PKS cluster to biosynthesise a 1,8-dihydroxynaphthalene (DHN)-type of pigment during sporulation with the influence of butyrolactone I under submerged culture. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I
Microorganisms 2017, 5(1), 12; https://doi.org/10.3390/microorganisms5010012
Received: 16 January 2017 / Revised: 1 March 2017 / Accepted: 9 March 2017 / Published: 14 March 2017
Cited by 5 | PDF Full-text (507 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along [...] Read more.
Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along with a global regulator LaeA. In A. terreus, the overexpression of LaeA has been observed to increase the biogenesis of the pharmaceutically-important secondary metabolite, lovastatin, while the role of the velvet family has not been studied. The secondary metabolism and conidiation of A. terreus have also been observed to be increased by butyrolactone I in a quorum-sensing manner. An enlightenment of the interplay of these regulators will give potential advancement to the industrial use of this fungus, as well as in resolving the pathogenic features. In this study, the Aspergillus terreus MUCL 38669 transcriptome was strand-specifically sequenced to enable an in-depth gene expression analysis to further investigate the transcriptional role of butyrolactone I in these processes. The sequenced transcriptome revealed intriguing properties of the velvet family transcripts, including the regulator laeA, and uncovered the velC gene in A. terreus. The reliability refining microarray gene expression analysis disclosed a positive regulatory role for butyrolactone I in laeA expression, as well as an influence on the expression of the canonical conidiation-regulating genes under submerged culture. All of this supports the suggested regulative role of butyrolactone I in A. terreus secondary metabolism, as well as conidiation.
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(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessReply Reply to the Comment on “Melanisation of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture? Microorganisms 2017, 5, 22”
Microorganisms 2017, 5(3), 36; https://doi.org/10.3390/microorganisms5030036
Received: 29 June 2017 / Revised: 30 June 2017 / Accepted: 30 June 2017 / Published: 4 July 2017
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Abstract
We are pleased that our paper has generated this discussion.[...] Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
Open AccessComment Comment on: “Melanisation of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture? Microorganisms 2017, 5, 22”
Microorganisms 2017, 5(2), 34; https://doi.org/10.3390/microorganisms5020034
Received: 23 May 2017 / Revised: 9 June 2017 / Accepted: 19 June 2017 / Published: 21 June 2017
Cited by 1 | PDF Full-text (506 KB) | HTML Full-text | XML Full-text
Abstract
A recent article by Palonen et al. describes the effect of butyrolactone I on the expression of a secondary metabolite biosynthesis gene cluster from Aspergillus terreus that shows similarities to fusarubin biosynthesis gene clusters from Fusarium species. The authors claim that two different [...] Read more.
A recent article by Palonen et al. describes the effect of butyrolactone I on the expression of a secondary metabolite biosynthesis gene cluster from Aspergillus terreus that shows similarities to fusarubin biosynthesis gene clusters from Fusarium species. The authors claim that two different types of pigments are formed in Aspergillus terreus conidia, whereby one pigment is termed a DOPA-type melanin and the second a DHN-type melanin. Unfortunately, the terminology of the classification of melanin-types requires revision as Asp-melanin present in A. terreus conidia is clearly distinct from DOPA-melanins. In addition, some hypotheses in this manuscript are based on questionable data published previously, resulting in incorrect conclusions. Finally, as biochemical data are lacking and metabolite production is only deduced from bioinformatics and transcriptomic data, the production of a second pigment type in A. terreus conidia appears highly speculative. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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