Fungal Physiology
This
group is a collaboration between the CBS Fungal Biodiversity Centre and Utrecht
University, Chair of Microbiology. Information on projects of this group at
Utrecht University can be found at:
http://www.bio.uu.nl/microbiology/
Fungal physiology is the basis
of biotope and global dispersion of fungal species. It determines the nutrients
it can use, the environmental conditions it can endure and its competitive
position in its ecosystem. The
ability of fungi to survive in every known biotope, both natural and man-made,
relies in part on their capacity to use a wide range of carbon sources. In
nature, many fungi degrade polymeric carbon sources (e.g. polysaccharides,
proteins, lignin) to use the monomeric components as carbon source. However, the
available carbon sources vary strongly in nature, both between biotopes and in
time. While some fungi have become specialists that focus on specific carbon
sources or specific biotopes, other have are more generalists that can grow in
many biotopes and use a large variety of carbon sources. Differences in
physiology may therefore also reflect species boundaries.
Degradation of polymeric carbon
sources occurs extracellularly by a broad range of enzymes, of which the
production is tightly controlled by a network of regulators. This enables fungi
to produce an enzyme mixture that is tailored specifically for the available
carbon sources at any given time. The released monomeric compounds are
transported into the cell and metabolized through a large variety of metabolic
pathways. These pathways are often co-regulated with the extracellular enzymes
that release the compounds entering the pathways, resulting in a highly complex
regulatory and metabolic network. To
study fungal physiology in relation to natural substrates it is therefore
necessary to address all these aspects of fungal biology: production of
extracellular enzymes, metabolic pathways and regulators controlling the fungal
response to the substrates present in the environment.
Fungal biodiversity with respect
to polysaccharide degradation
Enzymes involved in polysaccharide degradation are among the best studied
proteins in biology. Many genes encoding these enzymes have been cloned and
biochemical evidence for the function of many of the corresponding proteins has
been described. These enzymes can be divided into families based on amino acid
motifs in their sequence resulting in a comprehensive classification that is
available online through
www.cazy.org.
With the availability of more and more genome sequences, this database has grown
exponentially and a high demand for accurate function prediction of CAZy-related
genes has arisen. Analysis of fungal genome sequences with respect to
polysaccharide degradation enables determination of the hydrolytic potential of
fungi. In collaboration with the scientists responsible for the CAZy database,
Bernard Henrissat and Pedro Coutinho, we have shown that this hydrolytic
potential of fungi applied specifically to plant polysaccharides correlates very
well to the ability of the fungus to grown on polysaccharides and can explain
(in part) the biotope of a specific species. As we are adding more species to
our comparative analysis, the differences between the species with respect to
growth profile and biotope become more clear and can often be predicted based on
their genome sequence.
Improved understanding of fungal
physiology in relation to natural carbon sources
Very little is known about physiology of fungi in relation to natural carbon
sources as most physiological studies have been performed on defined media under
laboratory conditions or in bioreactors. To improve our understanding of fungal
physiology under natural conditions, in depth studies with model organisms are
required to provide the knowledge base for biodiversity studies. Two model
organisms have been chosen to study these processes. Both organisms have
publicly available genome sequences, transcriptomics and proteomics technology,
are readily transformed allowing gene introduction or inactivation and have a
long history of research:
-
Aspergillus
niger is one of the best studied organisms with respect to degradation of
natural carbon sources and is one of the most important industrial fungi in the
world. Many genes and their corresponding enzymes involved in polysaccharide
degradation have been studied in detail and 5 regulators related to this process
have already been characterized. Currently, three genome sequences are available
for A. niger as well as genome
sequences of 7 other Aspergillus
species, with several more in process.
-
Magnaporthe
grisea, also known as the rice blast fungus is one of the most important
plant pathogenic fungi worldwide. Its main impact is on rice production, causing
an annual crop loss that could feed millions of people. It contains many of the
systems related to plant polysaccharide degradation that have been studied in
A. niger, but initial results suggest
significant differences between the two species.
Detailed studies of the regulatory systems,
extracellular functions and metabolic pathways related to natural carbon sources
in these two fungi will provide additional targets for biodiversity studies in a
larger range of fungi.
Interaction between fungal
species in the environment
In their natural environment, fungal species co-exist with other organisms (e.g.
other fungi, bacteria). Some fungal species may compete for nutrients while
others may benefit from each other. Very little is known about the relationship
between fungal species and how they affect each other’s physiology. Studying the
ability of fungal species to co-exist, identifying competitive, synergistic and
parasitic relationships, and determining the effect of co-cultivation on
degradation of natural carbon sources will provide the first data into the
overall physiology of fungal populations. To this end, fungal species will be
co-cultivated on a range of substrates and analysis of their physiology will be
performed at the level of growth and morphology, cell biology, gene expression,
metabolism, production of extracellular enzymes and degradation of the natural
substrates. Combination of model fungi will be used as well as combinations of
fungal strains isolated from the same environment.