Tag Archives: Biofuels

The Genomes of Two Thermophilic and Biomass-Degrading Fungi, Thielavia terrestris and Myceliophthora thermophila

One of the hurdles to the production of cellulosic biofuel is the economic breakdown plant biomass.  Currently, fungi used to break down plant biomass operate at, or slightly above, room temperature.  Chemical reactions at room temperature proceed slowly, are less efficient, and may be riddled with contaminating fungi which lower the efficiency of the breakdown process.  One scientific goal is to increase the heat in bioreactors with the hopes of speeding up the degradation using efficient fungal enzymes that operate at higher temperatures.

In an effort find thermostable fungal degradative enzymes, researchers have sequenced the genomes of two fungi, Thielavia terrestris and Myceliophthora thermophila, known for their ability to survive at high temperatures, namely 40oC to 75oC.  A report entitled “Comparative Genomic Analysis of the Thermophilic Biomass-Degrading Fungi Myceliophthora thermophila and Thielavia terrestris” has been published online on October 2nd in the journal Nature Biotechnology.  (Image: Myceliophthora thermophila link)

The 38.7 Mbp genome of M. thermophila and the 36.9 Mbp genome of T. terrestris are the first thermophilic eukaryotes to have their genomes sequenced, and contain seven and six complete chromosomes, respectively.  The genome of M. thermophila contains 9,110 protein-coding genes and there are 9,813 such genes in the genome of T. terrestris.  Both filamentous Ascomycetes – placed in the class Sordariomycetes and family Chaetomiaceae – have a similar level of genomic organization, barring numerous translocations and transversions.  When considering the three species with sequenced genomes in the Chaetomiaceae, large portions of the genomes, some of which are greater than 6000 contiguous genes, are shared in syntenous blocks.

Enzymes for the breakdown of plant matter – which can include a wide array of materials from agricultural and forestry waste, recycled pulp and paper products, leaves, etc. – were discovered across the genomes of both T. terrestris and M. thermophila.  These enzymes include numerous carbohydrate-active proteins (CAZymes) which include enzymes in the glycoside hydrolase, polysaccharide lyase, carbohydrate esterase, and glycosyl transferase families.  With some slight differences in regard to the breakdown of specific plant polysaccharides, such as pectin, both fungi can be categorized as general decomposers with regards to their enzyme repertoire.

The researchers then tested the expression of some enzymes identified in these newly sequenced fungal genomes, as well as comparing their diversity to well characterized enzymes from Trichoderma reesei.  Differing from T. reesei, both M. thermophila and T. terrestris have exhibited a proliferation in the GH61 enzyme family, responsible for the degradation of plant cell wall polysaccharides, as well as the GH10 and GH11 xylanase gene families.  The researchers used RNA-Seq to compare the expression of these enzymes on differing plant materials, such as alfalfa and barley straw, which represented characteristic dicot and monocot plants, respectively.  While there are noticeable differences to the degradation of plant material from dicots and monocots by both T. terrestris and M. thermophila, orthologs from both fungal genomes show similar patterns of gene expression, particularly when growing on complex plant substrates.

Research commentaries on this publication can be found here and here.

Cracking Cellulose: A Enzyme That Exploits Biomass Components

A paper published in the recent issue of PNASInsights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components” by Quinlan et al. succeeds in characterizing an important aspect of the breakdown of cellulose by enzymes.  I’m interested in the use of cellulose in bioenergy purposes, but one of the major problems in its use is extreme recalcitrance of the polysaccaride.  By fully understanding the enzymatic mechanisms of the breakdown of cellulose we can surpass a major scientific and economic challenge for the effective release of bioenergy from biomass.

Cellulose is typically broken down by fungi employing a suite of different enzymes.  These enzymes are traditionally placed into two classes: endoglucanases and cellobiohydrolases.  In this paper, the authors identify the enzymatic abilities of a newly recognized enzyme class, called the GH61 glycoside hydrolases (see Harris et al. for more information on GH61 glycoside hydrolases).  The GH61 glycoside hydrolases greatly increase the efficiency of the endoglucanases and cellobiohydrolases and recent genome sequencing of brown rot fungi, such as Postia placenta, show numerous GH61 glycoside hydrolases.

The authors describe the 3D structure of a GH61 glycoside hydrolase from Thermoascus aurantiacus identifying the active site details and catalytic activity of the enzyme.  It was identified that the GH61 glycoside hydrolase enzymes are oxidizing agents and the authors show the direct degradation of cellulose.  Furthermore, the authors identify copper as the metal cofactor of the enzyme and show a unique methyl modification of a metal-coordinating histidine residue.

See here for commentary on the paper.