Scanning electron micrograph of Ceriporiopsis subvermispora mycelium on wood. Image: R. Blanchette, University of Minnesota |
Without
fungi and microbes to break down dead trees and leaf litter in nature, the
forest floor might look like a scene from television’s “Hoarders.”
Massive-scale
genome sequencing projects supported by the United States Department of Energy
(DOE) and being carried out at the DOE Joint Genome Institute (JGI) highlight
the importance of learning how the cellulose, hemicellulose, and lignin that
serve as a plant’s infrastructure can be broken down by these forest organisms
to extract needed nutrients. Among the fungi being studied are species that can
selectively break down the cell wall components cellulose and lignin—the number
one and two most abundant biopolymers on Earth.
In a
study published online in the Proceedings
of the National Academy of Sciences, an international team of
scientists presented a comparative genomic analysis of two white rot fungi
whose genomes were generated and annotated at the DOE JGI under the Community
Sequencing Program (CSP). Both the fungus Phanaerochaete chrysosporium
(sequenced by DOE JGI in 2004), and its close relative Ceriporiopisis
subvermispora are found all over the world and are of interest to bioenergy
researchers because they possess enzymes that can break down plant biomass and
could therefore be useful for accelerating biofuels production. The study
revealed substantial differences among the sets of genes involved in
lignocellulose degradation, providing further insight into the mechanics of how
white rots do their dirty work.
“The
fact that we have such a large group of people involved in this project is a
clear demonstration that there’s certainly interest in enzyme discovery,”
said study senior author and DOE JGI collaborator Dan Cullen of the U. S.
Department of Agriculture Forest Service, Forest Products Laboratory (FPL).
“In this particular case though, one would come away thinking more about
the role of white rot fungi in the carbon cycle. Lignin is a recalcitrant
compound in forest ecosystem biomass and very few fungi have the capability to
degrade lignin. Even fewer fungi have the ability to selectively remove lignin
at such an efficient rate. C. subvermispora is one exception in its ability
to do just that.”
Cullen
and his colleagues compared the fungal genomes to learn more about the basis of
C. subvermispora’s ability to selectively break down lignin.
Understanding this process of selective ligninolysis is of longstanding
interest to the pulp and paper industry. According to the American Forest &
Paper Association, approximately $175 billion worth of forest products such as
pulp and paper are produced annually, and account for five percent of the
nation’s GDP.
Analyzing
the diversity of wood-decaying fungi and cataloging enzymes involved in
lignocellulose degradation is one of the goals of the DOE JGI Fungal Genomics
Program led by Igor Grigoriev. “We are in the process of conducting
functional comparative genomics of more than 20 such fungi sequenced or
currently being sequenced at the DOE JGI,” he said. “This should
provide us a better understanding of the diverse and complex mechanisms of
lignocellulose degradation in fungi, the influence of these mechanisms on
carbon cycling in the forest ecosystem, and ultimately lead to improvements in
biopulping.”
Kent
Kirk, a former FPL researcher who is considered a leading figure in the study
of lignin degradation by fungi, provided perspective on how the current
research could impact the pulp and paper industry. “This grew out of
fundamental research by the University
of Minnesota and the FPL
where they applied the concept of ‘biopulping’—the partial decay of wood by
lignin-degrading fungi to decrease the energy required for mechanical pulping. Cerioporiopsis
subvermispora quickly became the ‘biopulper’ of choice.” Kirk
described how wood chips treated with the fungus for two weeks required 30%
less energy for pulping than untreated chips and how outdoor trials were
repeatedly successful at the 50-ton scale. “The technology has not yet
been commercially adopted, but as energy costs continue to rise, it should be
increasingly attractive for implementation,” Kirk said.
With
detailed biochemical analyses conducted by study co-author Angel Martinez’s
team at the Spanish National Research Council (CSIC) in Madrid, Spain,
the researchers found that the C. subvermispora genome had more
manganese peroxidases and laccase – enzymes that may speed the degradation of
lignin – than the P. chrysosporium genome. Martinez added that his group’s work also
revealed the presence of other lignin-degrading enzymes that had not previously
been found in C. subvermispora cultures.
“Since
Phanaerochaete doesn’t have laccases, they’re not absolutely necessary
for lignin degradation,” said Cullen, “though it could be that
they’re very important and play a role in Ceriporiopisis. The most
persuasive part of the data are the expansion and expression of the manganese
peroxidases, whose role in lignin degradation is more generally accepted.”
Cullen
added that the paper also suggests the cellulose-degrading portion of C.
subvermispora’s genome is “somewhat repressed” relative to P.
chrysosporium, another angle of further study to understand the Ceriporiopisis
genome’s selectivity for lignin. “It could be both,” he said,
“There’s not a simple clear final answer. To really make direct progress
on understanding the mechanism of selective lignin degradation, will require
development of more experimental tools, such as those for genetic analysis.
That is what’s next.”
