Fungal Genetics in Plant Biomass Conversion

Editorial

25 March 2022

Editorial: Fungal Genetics in Plant Biomass Conversion

Jiwei Zhang

Guodong Liu

and

Yu Fukasawa

1,529 views

4 citations

Editors

JIWEI ZHANG

University of Minnesota Twin Cities

Impact

Original Research

28 January 2021

Trichoderma reesei Isolated From Austrian Soil With High Potential for Biotechnological Application

Wolfgang Hinterdobler

, 4 more and

Monika Schmoll

Fungi of the genus Trichoderma are of high importance for biotechnological applications, in biocontrol and for production of homologous and heterologous proteins. However, sexual crossing under laboratory conditions has so far only been achieved with the species Trichoderma reesei, which was so far only isolated from tropical regions. Our isolation efforts aimed at the collection of Trichoderma strains from Austrian soils surprisingly also yielded 12 strains of the species T. reesei, which was previously not known to occur in Europe. Their identity was confirmed with tef1- and rpb2-sequencing and phylogenetic analysis. They could clearly be distinguished from tropical strains including the common laboratory wildtypes by UP-PCR and genetic variations adjacent to the mating type locus. The strains readily mated with reference strains derived from CBS999.97. Secreted cellulase and xylanase levels of these isolates were up to six-fold higher than those of QM6a indicating a high potential for strain improvement. The strains showed different responses to injury in terms of induction of sporulation, but a correlation to alterations in the nox1-gene sequence was not detected. Several synonymous SNPs were found in the sequence of the regulator gene noxR of the soil isolates compared to QM6a. Only in one strain, non-synonymous SNPs were found which impact a PEST sequence of NoxR, suggesting altered protein stability. The availability of sexually fertile strains from middle Europe naturally producing decent amounts of plant cell wall degrading enzymes opens up novel perspectives for non-GMO strain improvement and biological pretreatment of plant biomass for bioethanol production. Moreover, the varied response of these strains to injury in terms of sporulation, which is independent of Nox1 and NoxR suggests that additional regulators impact this phenomenon in T. reesei.

8,687 views

14 citations

Secondary metabolite (SM) synthesis clusters in Gloeophyllum trabeum that contain at least one SM-synthesizing gene that is upregulated in interacting hyphae relative to 0–5 mm behind the leading hyphal front of single species cultures. Arrows represent genes with JGI protein ID number over relevant genes. Fold changes in expression levels (IZ/Gt_0–5) are shown in red over each SM synthesis-related gene. JGI protein ID numbers are shown on each annotated gene on the secondary metabolite synthesis cluster. PKS, Polyketide synthases; OR, oxidoreductases; p450, Cytochrome p450; STS, sesquiterpene synthases; NRPS, Non-ribosomal peptide synthase; TR, Transporter.

Original Research

28 July 2020

Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms

Gerald N. Presley

, 2 more and

Jonathan S. Schilling

4,533 views

14 citations

Original Research

14 July 2020

Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117

Jia-Xiang Li

, 6 more and

Xin-Qing Zhao

8,287 views

36 citations

Graphic summary of this study. (A) Compared to T. reesei, C. thermophilum degrades celluloses more efficiently with lower production of cellulases. (B) The proposed model of the mechanism for higher production of cellulases in Tr-Ctcbh1 strains. Replacement of Tr-cbh1 with Ct-cbh1 gene in T. reesei first increased the CBH1 activity, which could cause instantaneous accumulation of cellobiose. This extra cellobiose might function as a possible inducer to trigger more induction and expression of cellulases genes.

Original Research

14 July 2020

Improved Production of Majority Cellulases in Trichoderma reesei by Integration of cbh1 Gene From Chaetomium thermophilum

Xianzhang Jiang

, 5 more and

Lina Qin

4,573 views

23 citations

Co-expression of LPMO and LMW hydroquinone pathways at an early brown rot stage in G. trabeum. (A) The hydroquinone chelator synthesis pathway and the enzyme homologs catalyzing each step are proposed based on standard pathways. Genes that were significantly upregulated (*, FDR < 0.05 by RNA-seq) in early brown rot basically covered all the required key enzyme components of the pathway, although several OMT, 3HB6H and SAH genes were clearly upregulated at late decay stages (x, FDR < 0.05) (B). Expression timing of G. trabeum LPMO genes showed that AA9a was significantly upregulated in early brown rot stages, and these were co-expressed with genes for metabolites produced in proposed pathway for hydroquinone synthesis. (C) Expression levels for GtrAA9 genes during early-, mid- and late-decay stages.

Original Research

24 June 2020

Nanostructural Analysis of Enzymatic and Non-enzymatic Brown Rot Fungal Deconstruction of the Lignocellulose Cell Wall†

Yuan Zhu

, 7 more and

Barry Goodell

Brown rot (BR) decay mechanisms employ carbohydrate-active enzymes (CAZymes) as well as a unique non-enzymatic chelator-mediated Fenton (CMF) chemistry to deconstruct lignocellulosic materials. Unlike white rot fungi, BR fungi lack peroxidases for lignin deconstruction, and also lack some endoglucanase/cellobiohydrolase activities. The role that the CMF mechanism plays in “opening up” the wood cell wall structure in advance of enzymatic action, and any interaction between CMF constituents and the selective CAZyme suite that BRs possess, is still unclear. Expression patterns for CMF redox metabolites and lytic polysaccharide monooxygenase (LPMO–AA9 family) genes showed that some LPMO isozymes were upregulated with genes associated with CMF at early stages of brown rot by Gloeophyllum trabeum. In the structural studies, wood decayed by the G. trabeum was compared to CMF-treated wood, or CMF-treated wood followed by treatment with either the early-upregulated LPMO or a commercial CAZyme cocktail. Structural modification of decayed/treated wood was characterized using small angle neutron scattering. CMF treatment produced neutron scattering patterns similar to that of the BR decay indicating that both systems enlarged the nanopore structure of wood cell walls to permit enzyme access. Enzymatic deconstruction of cellulose or lignin in raw wood samples was not achieved via CAZyme cocktail or LPMO enzyme action alone. CMF treatment resulted in depolymerization of crystalline cellulose as attack progressed from the outer regions of individual crystallites. Multiple pulses of CMF treatment on raw wood showed a progressive increase in the spacing between the cellulose elementary fibrils (EFs), indicating the CMF eroded the matrix outside the EF bundles, leading to less tightly packed EFs. Peracetic acid delignification treatment enhanced subsequent CMF treatment effects, and allowed both enzyme systems to further increase spacing of the EFs. Moreover, even after a single pulse of CMF treatment, both enzymes were apparently able to penetrate the cell wall to further increase EF spacing. The data suggest the potential for the early-upregulated LPMO enzyme to work in association with CMF chemistry, suggesting that G. trabeum may have adopted mechanisms to integrate non-enzymatic and enzymatic chemistries together during early stages of brown rot decay.

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41 citations

%Lignin loss relative to%Density loss (L/D) in aspen wood decayed by fungi with distinct nutritional modes, restricted to Class ll/lll decay. A O.S threshold (dashed line) distinguishing brown and white rot proposed by Worrall et al. (1997; “Wor”), and validated in Schilling et al. (2015; “Sch”), is complemented in this study (“New”). Gene count correlations with L/D are shown for the sum of genes from Table 2, including a separate correlation for PODs.

Original Research

12 June 2020

Using Wood Rot Phenotypes to Illuminate the “Gray” Among Decomposer Fungi

Jonathan S. Schilling

, 3 more and

Robert A. Blanchette

Wood-decomposing fungi use distinct strategies to deconstruct wood that can significantly vary carbon release rates and fates. White and brown rot-type fungi attack lignin as a prerequisite to access carbohydrates (white rot) or selectively remove carbohydrates (brown rot). Soft rot fungi use less well-studied mechanisms to deconstruct wood (e.g., cavitation and erosion). These fungi often co-exist in nature, creating a balance in carbon turnover that could presumably “tip” in a changing climate. There is no simple genetic marker, however, to distinguish fungi by rot types, and traditional black and white distinctions (brown and white, in this case) cannot explain a spectrum of “gray” carbon loss possibilities. In this study, we tested 39 wood-degrading fungal strains along this spectrum of rot types. We tracked wood mass loss and chemical changes in aspen blocks in early- to mid-decay stages, including three signatures of fungal nutritional mode measured from wood rather than from fungus: dilute alkali solubility, water-soluble monosaccharides, and lignin loss (%) relative to density loss (%) (L/D). Results were then plotted relative to rot types and correlated with gene counts, combining new data with past results in some cases. Results yielded a novel distinction in soluble monosaccharide patterns for brown rot fungi, and reliable distinctions between white and brown rot fungi, although soft rot fungi were not as clearly distinguished as suggested in past studies. Gene contents (carbohydrate-active enzymes and peroxidases) also clearly distinguished brown and white rot fungi, but did not offer reliable correlation with lignin vs. carbohydrate selectivity. These results support the use of wood residue chemistry to link fungal genes (with known or unknown function) with emergent patterns of decomposition. Wood signatures, particularly L/D, not only confirm the rot type of dominant fungi, but they offer a more nuanced, continuous variable to which we can correlate genomic, transcriptomic, and secretomic evidence rather than limit it to functional categories as distinct “bins.”

5,211 views

40 citations