the interaction between fungi and their environment is of major importance for saprobes , symbionts and pathogens and has been a topic of study for many decades .
currently , genome sequences are available for many fungi , including saprobes ( espagne et al .
. 2005 , kmper et al . 2006 ) , human pathogens ( nierman et al . 2005 ) and mycorrhizae ( martin et al . 2008 , 2010 ) .
sequencing of additional fungal genomes is occurring at an increasing rate in many centres all over the world , but the two largest fungal sequencing programs are running in the us at the joint genome institute of the department of energy ( http://genome.jgi-psf.org/programs/fungi/index.jsf ) and the broad institute ( http://www.broadinstitute.org/scientific-community/science/projects/fungal-genome-initiative/fungal-genome-initiative ) . these initiatives are providing genome resources for a representative subset of the fungi , enabling full - genome comparison of fungal biodiversity .
the availability of fungal genome sequences was followed by the development of post - genomic resources , of which transcriptomics was the first .
initially transcriptomics was mainly available for fungal species which were studied by large consortia of scientists , due to the high costs involved in developing micro - arrays .
most papers on fungal transcriptomics have therefore addressed species such as saccharomyces cerevisiae , various aspergillus species , candida albicans , neurospora crassa and magnaporthe grisea ( andersen et al .
however , with the development of rna ( cdna ) sequencing , transcriptomics has become available for any species that has a sequenced genome and transcriptomic studies are now often included in genome papers .
proteomics was soon to follow and many studies on fungal proteomics have been reported in the last eight years ( acero et al .
2004 , ho et al . 2002 , kim et al . 2003 , 2004 , lim et al .
these post - genomic studies have been aimed at many aspects of fungal biology . in this paper
they were based on presentations at a special interest group meeting during imc9 in edinburgh in august 2010 .
aspergillus oryzae xlnr was phosphorylated at low level in the absence of d - xylose , and was hyper - phosphorylated in its presence .
removal of d - xylose caused dephosphorylation of the hyper - phosphorylated forms leading to accumulation of less phosphorylated forms .
while aspergillus niger and aspergillus nidulans have two xlnr homologs , arar and gala , a. oryzae has only arar involved in l - arabinose catabolism .
dna microarray analysis for determining xlnr targets was performed by expression profiles of the xlnr overproducer and the xlnr deletion mutant after exposure to d - xylose for 30 min .
the analysis revealed 75 genes as the possible targets of xlnr , including 32 glycoside hydrolases and three esterases for degradation of xylan and cellulose , seven transporters , and three genes for d - xylose catabolism ( noguchi et al .
one compared expression profiles of l - arabinose induced and un - induced conditions , and the other compared those in the wild type and the arar deletion mutant under l - arabinose induced conditions . by combination of the results ,
1 ) , including 16 glycoside hydrolases , seven transporters , and several candidate genes for l - arabinose catabolism .
the candidate genes for l - arabinose catabolism were expressed as his - tagged proteins in escherichia coli .
analysis of substrate specificity of the recombinant enzymes led to identification of l - arabinose reductase and l - xylulose reductase in a. oryzae .
the dna microarray analysis contributed substantially to an in depth understanding of the degradation and utilization of hemicellulose by a. oryzae .
fungal colonies do not behave as uniform entities , but show differentiation for many aspects of physiology .
the first report of this phenomenon described that protein secretion and growth only took place the periphery of colonies of aspergillus niger grown on maltose ( wsten et al .
a specific growth system was developed called the ring - plate system ( levin et al .
this system consists of a round polycarbonate plate with concentric channels that are filled with liquid medium and a perforated polycarbonate membrane ( fig .
2 ) . this membrane allows transport of nutrients and proteins , but the pores are too small to allow passage of fungal hyphae . using this system
it was shown that not only protein secretion and growth , but also overall gene expression is highly differentiated in colonies of a. niger grown on maltose or d - xylose ( levin et al .
part of this differentiation could be attributed to depletion of the carbon source in the zones towards the centre of the colony .
for instance , genes involved in nitrate utilisation were only expressed in the periphery of the colony , even though there was no significant difference in the nitrate concentration in the zones ( levin et al .
, fungi do not grow on high levels of pure mono- or disaccharides , but rather on mixtures of polymeric compounds ( e.g. plant biomass ) . to release the monomeric carbon sources that can be taken up by the fungal cell
the complexity of these mixtures was illustrated by a review presenting an overview of aspergillus enzymes involved in plant cell wall degradation ( de vries & visser 2001 ) .
this indicates that in nature fungi are nt subjected to a gradual reduction of a single carbon source , but more likely to substrates with changing compositions and levels . to study zonal differentiation on natural substrates ,
a. niger was grown on the ring - plate system using sugar beet pulp as a carbon source .
sugar beet pulp is a waste product of the sugar industry and consists mainly of cellulose , xyloglucan and pectin .
transcriptomic analysis using whole genome micro arrays for a. niger demonstrated that differentiation occurred to a lesser extent than on d - xylose and maltose ( benoit & de vries , unpubl . ) .
in addition , growth and protein secretion were observed throughout the colony , rather than only at the periphery ( benoit & de vries , unpubl . ) .
this life - style , breaking down and utilizing complex biopolymers , requires a variety of hydrolytic enzymes secreted into the immediate environment of the fungus .
examination of the variations in the secretome of a fungus when confronted with different complex or simple substrates can reveal what the fungus is capable of utilizing and which secreted enzymes in its genome are expressed under particular conditions .
we grew the zygomycete phycomyces blakesleeanus and the ascomycete thielavia terrestris on four complex carbon sources and glucose as a control using a defined medium of inorganic nutrients as a base .
the complex carbon sources were alder sawdust , pine sawdust , wheat bran and soybean hulls representing hardwoods , softwoods , grasses and dicotyledonous herbaceous plants respectively .
the cultures were incubated at 30 c ( p. blakesleeanus ) or 40 c ( t. terrestris ) for four days and the fungal and plant solid material was removed by filtration through miracloth . the resulting liquid constituted the secretomes of the fungi .
the proteins were concentrated on 10 kda membranes , reduced and carboxamidomethylated , then digested with trypsin .
the peptide solution was cleaned on disposable reverse phase ( c18 ) columns and analyzed by high throughput liquid chromatography mass spectrometry ( lc - ms ) proteomics .
the resulting ms and ms / ms spectra ( molecular ion and fragmentation patterns , respectively ) were analyzed against the protein databases of these two fungi using the sequest program ( yates et al .
the proteomics results for the zygomycete p. blakesleeanus suggest a bias towards scavenging protein with many proteases expressed under the different conditions ( table 1 ) , but relatively few glycoside hydrolases .
these proteomics observations are consistent with the paucity of glycoside hydrolase genes in this zygomycete s genome relative to saprobic ascomycetes .
the ascomycete t. terrestris expressed a wide array of glycoside hydrolases , and some proteases , on the various substrates .
these proteomics results are consistent with the rich diversity of cazymes found in saprobic ascomycete genomes ( e.g. martinez et al .
proteomics is a powerful technique for investigating which proteins are actually expressed and secreted by fungi when they are presented with different substrates in their environment .
infection of maize by the fungal biotroph ustilago maydis leads to formation of tumors in basically all aerial parts of the plant .
transcriptome profiling of u. maydis during pathogenic development was performed using a custom affymetrix gene - chip microarray .
this approach , together with sequencing of the u. maydis genome , identified 12 gene clusters encoding secreted effectors that are transcriptionally upregulated specifically during biotrophic interaction ( kmper et al .
deletion mutants for five of these gene clusters were altered in tumor formation , demonstrating the potential of transcript profiling for identifying virulence factors ( kmper et al .
2006 ) a major step in understanding the impact of u. maydis infection on maize gene expression was achieved by transcriptome profiling of maize seedling leaves at different stages of infection ( doehlemann et al .
use of the affymetrix maize genome array identified a broad reprogramming of the maize primary- and secondary metabolism , particularly modulation of hormone signaling pathways as well as a shutdown of photosynthesis ( doehlemann et al .
a major finding of this study was the attenuation of plant defences as soon as biotrophy has been established ( doehlemann et al .
obviously there are fundamental differences between the various maize organs that u. maydis transforms into tumors .
therefore , transcriptome profiling was applied to study whether the distinctive developmental changes necessary for converting maize primordia to tumors would require organ - specific gene expression . to enable
simultaneous transcript profiling of host and pathogen , a two organism microarray was designed using the agilent platform ( skibbe et al .
expression data from infected seedling leaf , adult leaf , and tassel revealed organ - specific expression programs of both interaction partners .
in particular u. maydis genes encoding secreted effector proteins appeared to underlie organ - specific regulation ( skibbe et al .
moreover , u. maydis mutants deleted for clusters of secreted effectors ( kmper et al . 2006 ) showed significant differences in virulence depending on the infected maize organ ( skibbe et al .
together , these results show that tumor formation requires organ - specific gene expression by both partners .
this finding of organ - specific activity of pathogen effectors set a new paradigm in plant pathology and further demonstrates the power of transcriptome profiling in understanding of complex organismic interactions .
aspergillus oryzae xlnr was phosphorylated at low level in the absence of d - xylose , and was hyper - phosphorylated in its presence .
removal of d - xylose caused dephosphorylation of the hyper - phosphorylated forms leading to accumulation of less phosphorylated forms .
while aspergillus niger and aspergillus nidulans have two xlnr homologs , arar and gala , a. oryzae has only arar involved in l - arabinose catabolism .
dna microarray analysis for determining xlnr targets was performed by expression profiles of the xlnr overproducer and the xlnr deletion mutant after exposure to d - xylose for 30 min .
the analysis revealed 75 genes as the possible targets of xlnr , including 32 glycoside hydrolases and three esterases for degradation of xylan and cellulose , seven transporters , and three genes for d - xylose catabolism ( noguchi et al .
one compared expression profiles of l - arabinose induced and un - induced conditions , and the other compared those in the wild type and the arar deletion mutant under l - arabinose induced conditions . by combination of the results ,
1 ) , including 16 glycoside hydrolases , seven transporters , and several candidate genes for l - arabinose catabolism .
the candidate genes for l - arabinose catabolism were expressed as his - tagged proteins in escherichia coli .
analysis of substrate specificity of the recombinant enzymes led to identification of l - arabinose reductase and l - xylulose reductase in a. oryzae .
the dna microarray analysis contributed substantially to an in depth understanding of the degradation and utilization of hemicellulose by a. oryzae .
fungal colonies do not behave as uniform entities , but show differentiation for many aspects of physiology .
the first report of this phenomenon described that protein secretion and growth only took place the periphery of colonies of aspergillus niger grown on maltose ( wsten et al .
a specific growth system was developed called the ring - plate system ( levin et al .
this system consists of a round polycarbonate plate with concentric channels that are filled with liquid medium and a perforated polycarbonate membrane ( fig .
2 ) . this membrane allows transport of nutrients and proteins , but the pores are too small to allow passage of fungal hyphae . using this system
it was shown that not only protein secretion and growth , but also overall gene expression is highly differentiated in colonies of a. niger grown on maltose or d - xylose ( levin et al .
part of this differentiation could be attributed to depletion of the carbon source in the zones towards the centre of the colony . however , this was not the case for all gene systems .
for instance , genes involved in nitrate utilisation were only expressed in the periphery of the colony , even though there was no significant difference in the nitrate concentration in the zones ( levin et al .
, fungi do not grow on high levels of pure mono- or disaccharides , but rather on mixtures of polymeric compounds ( e.g. plant biomass ) . to release the monomeric carbon sources that can be taken up by the fungal cell
the complexity of these mixtures was illustrated by a review presenting an overview of aspergillus enzymes involved in plant cell wall degradation ( de vries & visser 2001 ) .
this indicates that in nature fungi are nt subjected to a gradual reduction of a single carbon source , but more likely to substrates with changing compositions and levels . to study zonal differentiation on natural substrates ,
a. niger was grown on the ring - plate system using sugar beet pulp as a carbon source .
sugar beet pulp is a waste product of the sugar industry and consists mainly of cellulose , xyloglucan and pectin .
transcriptomic analysis using whole genome micro arrays for a. niger demonstrated that differentiation occurred to a lesser extent than on d - xylose and maltose ( benoit & de vries , unpubl . ) .
in addition , growth and protein secretion were observed throughout the colony , rather than only at the periphery ( benoit & de vries , unpubl . ) .
this life - style , breaking down and utilizing complex biopolymers , requires a variety of hydrolytic enzymes secreted into the immediate environment of the fungus .
examination of the variations in the secretome of a fungus when confronted with different complex or simple substrates can reveal what the fungus is capable of utilizing and which secreted enzymes in its genome are expressed under particular conditions .
we grew the zygomycete phycomyces blakesleeanus and the ascomycete thielavia terrestris on four complex carbon sources and glucose as a control using a defined medium of inorganic nutrients as a base .
the complex carbon sources were alder sawdust , pine sawdust , wheat bran and soybean hulls representing hardwoods , softwoods , grasses and dicotyledonous herbaceous plants respectively .
the cultures were incubated at 30 c ( p. blakesleeanus ) or 40 c ( t. terrestris ) for four days and the fungal and plant solid material was removed by filtration through miracloth . the resulting liquid constituted the secretomes of the fungi .
the proteins were concentrated on 10 kda membranes , reduced and carboxamidomethylated , then digested with trypsin .
the peptide solution was cleaned on disposable reverse phase ( c18 ) columns and analyzed by high throughput liquid chromatography mass spectrometry ( lc - ms ) proteomics .
the resulting ms and ms / ms spectra ( molecular ion and fragmentation patterns , respectively ) were analyzed against the protein databases of these two fungi using the sequest program ( yates et al .
the proteomics results for the zygomycete p. blakesleeanus suggest a bias towards scavenging protein with many proteases expressed under the different conditions ( table 1 ) , but relatively few glycoside hydrolases .
these proteomics observations are consistent with the paucity of glycoside hydrolase genes in this zygomycete s genome relative to saprobic ascomycetes .
the ascomycete t. terrestris expressed a wide array of glycoside hydrolases , and some proteases , on the various substrates . the cellulose related cazymes
these proteomics results are consistent with the rich diversity of cazymes found in saprobic ascomycete genomes ( e.g. martinez et al .
proteomics is a powerful technique for investigating which proteins are actually expressed and secreted by fungi when they are presented with different substrates in their environment .
infection of maize by the fungal biotroph ustilago maydis leads to formation of tumors in basically all aerial parts of the plant .
transcriptome profiling of u. maydis during pathogenic development was performed using a custom affymetrix gene - chip microarray .
this approach , together with sequencing of the u. maydis genome , identified 12 gene clusters encoding secreted effectors that are transcriptionally upregulated specifically during biotrophic interaction ( kmper et al .
deletion mutants for five of these gene clusters were altered in tumor formation , demonstrating the potential of transcript profiling for identifying virulence factors ( kmper et al .
2006 ) a major step in understanding the impact of u. maydis infection on maize gene expression was achieved by transcriptome profiling of maize seedling leaves at different stages of infection ( doehlemann et al .
use of the affymetrix maize genome array identified a broad reprogramming of the maize primary- and secondary metabolism , particularly modulation of hormone signaling pathways as well as a shutdown of photosynthesis ( doehlemann et al .
a major finding of this study was the attenuation of plant defences as soon as biotrophy has been established ( doehlemann et al .
obviously there are fundamental differences between the various maize organs that u. maydis transforms into tumors .
therefore , transcriptome profiling was applied to study whether the distinctive developmental changes necessary for converting maize primordia to tumors would require organ - specific gene expression . to enable
simultaneous transcript profiling of host and pathogen , a two organism microarray was designed using the agilent platform ( skibbe et al .
expression data from infected seedling leaf , adult leaf , and tassel revealed organ - specific expression programs of both interaction partners .
in particular u. maydis genes encoding secreted effector proteins appeared to underlie organ - specific regulation ( skibbe et al .
moreover , u. maydis mutants deleted for clusters of secreted effectors ( kmper et al . 2006 ) showed significant differences in virulence depending on the infected maize organ ( skibbe et al .
together , these results show that tumor formation requires organ - specific gene expression by both partners .
this finding of organ - specific activity of pathogen effectors set a new paradigm in plant pathology and further demonstrates the power of transcriptome profiling in understanding of complex organismic interactions .
 fungi inhabit every natural and anthropogenic environment on earth . 
 they have highly varied life - styles including saprobes ( using only dead biomass as a nutrient source ) , pathogens ( feeding on living biomass ) , and symbionts ( co - existing with other organisms ) . these distinctions are not absolute as many species employ several life styles ( e.g. saprobe and opportunistic pathogen , saprobe and mycorrhiza ) . to efficiently survive in these different and often changing environments , fungi need to be able to modify their physiology and in some cases 
 will even modify their local environment . 
 understanding the interaction between fungi and their environments has been a topic of study for many decades . 
 however , recently these studies have reached a new dimension . 
 the availability of fungal genomes and development of post - genomic technologies for fungi , such as transcriptomics , proteomics and metabolomics , have enabled more detailed studies into this topic resulting in new insights . 
 based on a special interest group session held during imc9 , this paper provides examples of the recent advances in using ( post-)genomic approaches to better understand fungal interactions with their environments . 
INTRODUCTION
CONTRIBUTIONS
Transcriptional regulation of genes involved in hemicellulose and cellulose utilization in 
Zonal differentiation in sugar beet grown colonies of 
Secretomes: Proteomic clues to fungal life-style choice
Transcriptome profiling of the 