Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation

Yakovlev, Igor; Hietala, Ari M.; Courty, Pierre‐Emmanuel; Lundell, Taina; Solheim, Halvor; Fossdal, Carl Gunnar

doi:10.1016/j.fgb.2013.04.011

Cited by 35 publications

(28 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S6). These observations suggest that fosmids recovered in the PemrR-GFP biosensor screen confer lignin transformation phenotypes with different end product profiles, similar to observations made for fungal lignin transformation (22,23).…”

Section: Significancesupporting

confidence: 73%

Metagenomic scaffolds enable combinatorial lignin transformation

Strachan

Singh

VanInsberghe

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles.environmental genomics | synthetic biology L ignin is the second-most abundant biopolymer on Earth and a promising feedstock for deriving energy, fine chemicals, and structural materials from renewable plant resources (1, 2). The synthesis of lignin occurs within plant cell walls by free radical reactions that cross-link phenylpropanoids into a heterogeneous matrix that is resistant to microbial and chemical attack (3). Lignin recalcitrance is further reflected in the deposition of coal throughout the Carboniferous period before the emergence of fungal enzymes associated with lignolysis in Permian forest soil ecosystems (4). To date, fungi are the most widely studied lignindegrading microbes and are the major source of lignin-transforming enzymes, including laccases, manganese-dependent peroxidases, and lignin peroxidases (5-9). Functional characterization of these metalloenzymes is consistent with a model of lignin degradation based on oxidative combustion mediated by a broad range of small molecule oxidants, such as veratryl alcohol and Mn(III) (9).Despite this mechanistic understanding, however, there are numerous challenges associated with engineering lignin bioprocess streams, including the genetic intractability of many fungal systems and barriers to scale-up expression of active fungal-derived enzymes in heterologous systems, such as Escherichia coli. Although a handful of bacterial isolates, including Enterobacter lignolyticus SCF1 and Rhodococcus jostii RHA1, encode lignin-transforming phenotypes, the functional diversity of bacterial lignin-transforming enzymes in the ...

show abstract

Section: Significancesupporting

confidence: 73%

Metagenomic scaffolds enable combinatorial lignin transformation

Strachan

Singh

VanInsberghe

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…H . irregulare is known to remove lignin and hemicellulose prior to breaking down cellulose [62], which suggests that deconstruction of glucomannan network may be an initial step that allows hyphal penetration across the plant cell walls. The considerable reduction of glucomannan viscosity shown by Hi LPMO9I suggests that this enzyme could be recruited for the disruption of glucomannan network to facilitate the hyphal penetration.…”

Section: Discussionmentioning

confidence: 99%

Side-by-side biochemical comparison of two lytic polysaccharide monooxygenases from the white-rot fungus Heterobasidion irregulare on their activity against crystalline cellulose and glucomannan

et al. 2018

View full text Add to dashboard Cite

Our comparative studies reveal that the two lytic polysaccharide monooxygenases HiLPMO9B and HiLPMO9I from the white-rot conifer pathogen Heterobasidion irregulare display clear difference with respect to their activity against crystalline cellulose and glucomannan. HiLPMO9I produced very little soluble sugar on bacterial microcrystalline cellulose (BMCC). In contrast, HiLPMO9B was much more active against BMCC and even released more soluble sugar than the H. irregulare cellobiohydrolase I, HiCel7A. Furthermore, HiLPMO9B was shown to cooperate with and stimulate the activity of HiCel7A, both when the BMCC was first pretreated with HiLPMO9B, as well as when HiLPMO9B and HiCel7A were added together. No such stimulation was shown by HiLPMO9I. On the other hand, HiLPMO9I was shown to degrade glucomannan, using a C4-oxidizing mechanism, whereas no oxidative cleavage activity of glucomannan was detected for HiLPMO9B. Structural modeling and comparison with other glucomannan-active LPMOs suggest that conserved sugar-interacting residues on the L2, L3 and LC loops may be essential for glucomannan binding, where 4 out of 7 residues are shared by HiLPMO9I, but only one is found in HiLPMO9B. The difference shown between these two H. irregulare LPMOs may reflect distinct biological roles of these enzymes within deconstruction of different plant cell wall polysaccharides during fungal colonization of softwood.

show abstract

“…H. irregulare also encodes 18 multicopper oxidases, 13 of which are laccases sensu stricto (Floudas et al, 2012). This is the highest amount reported from any white rot fungi and similar to C. cinerea (Yakovlev et al, 2013). Twelve of the oxidases are upregulated when H. irregulare is growing on reaction zone wood rich in phenolic compounds.…”

Section: Gene Environmentmentioning

confidence: 94%

“…The pathogenicity of Heterobasidion is manifested by the ability to overcome this and continue to colonise and degrade plant tissue. The ligninolytic repertoire includes six short hybridtype Mn peroxidases and one generic peroxidase and one pseudogene (Yakovlev et al, 2013). H. irregulare also encodes 18 multicopper oxidases, 13 of which are laccases sensu stricto (Floudas et al, 2012).…”

Section: Gene Environmentmentioning

confidence: 99%