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Table 2 Functional categorization of selected genes

From: RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior

Number Name Known description, putative function or ortholog function
B30 up-regulation
 Secondary metabolism
AFUA_3G00840   FAD-dependent oxygenase, required for asperfuranone biosynthesis in A. nidulans (afoF) FAD-dependant oxygenase; secreted protein
AFUA_3G12910 hasC O-methyltransferase GliM-like, orthologous member of the “has” secondary metabolite biosynthetic gene cluster of strain A1163. [67]
AFUA_3G12930 hasE dimethylallyl tryptophan synthase SirD-like, orthologous member of the “has” secondary metabolite biosynthetic gene cluster of strain A1163. [67]
 Transcriptional control
AFUA_5G06190 steA sexual development transcription factor, involved in sexual development
AFUA_5G05610   putative cell cycle control protein Cwf14/Bud31, ortholog(s) have role in cellular bud site selection
AFUA_1G12940 sakA MAP kinase SakA, nitrogen sensing, is induced upon carbon and nitrogen starvation [52]
 Transport
AFUA_1G12620 aflT MFS toxin efflux pump
AFUA_7G04290   GapA, putative amino acid transporter
AFUA_8G02200   proline permease, putative amino acid transporter
 Stress response
AFUA_5G06520   low-temperature viability protein ltv1, ortholog(s) have role in cellular response to oxidative stress, response to osmotic stress
AFUA_5G11230 rasA RAS small monomeric GTPase RasA, involved in cell wall integrity
 Chaperone and protein folding activity
AFUA_2G02320   Hsp70 chaperone (BiP)
AFUA_4G03650   ribosome associated DnaJ chaperone Zuotin,
AFUA_8G03930 hscA Hsp70 chaperone HscA, Yap1-dependent induction in response to hydrogen peroxide; hypoxia induced protein
AFUA_2G16290   DnaJ domain protein Mas5, ortholog(s) have endoplasmic reticulum localization
AFUA_4G12360   prefoldin subunit 1, has domain(s) with predicted unfolded protein binding activity, role in protein folding and prefoldin complex localization
 Detoxification
AFUA_4G12990 trr1 thioredoxin reductase Trr1/Trr2
AFUA_4G00930   CorA family metal ion transporter, Mg transport
AFUA_2G13080   Nudix/MutT family protein, ortholog(s) have hydrolase activity
AFUA_1G12620 aflT MFS toxin efflux pump
 Lipid acid and isoprenoid metabolism
AFUA_8G04080 badA betaine aldehyde dehydrogenase, involved in glycin betain biosynthesis [45]
AFUA_8G04090 codA choline oxidase, involved in glycin betain biosynthesis [45]
B30 down-regulation
 Secondary metabolism:
AFUA_1G10380 nrps1 nonribosomal peptide synthase Pes1, essential for fumigaclavine C biosynthesis [47]
AFUA_3G03350 sidE nonribosomal peptide synthase SidE, involved in production of fumarylalanine [48]
 Transcription
AFUA_1G12332   jumonji family transcription factor, has domain(s) with predicted zinc ion binding activity
AFUA_1G13750   C2H2 transcription factor Rpn4, proteasomal regulator in S. cervisiae
AFUA_1G15230   C6 transcription factor, ortholog(s) have role in conidiophore development, conidium formation, hyphal growth
AFUA_1G16460   bZIP transcription factor (LziP), ortholog(s) have role in asexual sporulation, sexual sporulation resulting in formation of a cellular spore
AFUA_2G11780   CreA, C2H2 transcription factor
  AFUA_2G13260 medA MedA, transcriptional regulator of adherence, host cell interactions and virulence; required for wild-type levels of conidiation
  AFUA_2G14110   sulfur metabolite repression control protein, ortholog(s) have protein binding, bridging, ubiquitin binding activity
  AFUA_2G14680 flbB Bzip developmental regulator; role in asexual development, gliotoxin production
  AFUA_2G16230   C2H2 finger domain protein, has domain(s) with predicted DNA binding, zinc ion binding activity, role in transcription
  AFUA_2G17220   C2H2 transcription factor (AmdX), ortholog(s) have sequence-specific DNA binding activity, role in regulation of transcription
  AFUA_3G02000   farB like, C6 transcription factor Ctf1B-like, putatively involved in fatty acid degradation
  AFUA_3G05760   C6 transcription factor (Fcr1)
  AFUA_3G06250   RNA polymerase II mediator complex component, has domain(s) with predicted RNA polymerase II transcription cofactor activity
  AFUA_3G11250 ace2 C2H2 transcription factor (Swi5), with a role in conidiophore development, pigment production, germination and virulence
  AFUA_3G12940 hasF C6 transcription factor, orthologous member of the “has” secondary metabolite biosynthetic gene cluster of strain A1163. [67]
  AFUA_4G03960 farA C6 transcription factor Ctf1A, with a role in beta oxidation of long-chain fatty acids
  AFUA_6G12160   C6 transcription factor
 Cell wall
  AFUA_6G06340 gfa1 glucosamine-fructose-6-phosphate transaminase, chitin production
  AFUA_2G01170 gel1 1,3-beta-glucanosyltransferase, biosynthesis of fungal cell wall [91]
  AFUA_2G05340 gel4 1,3-beta-glucanosyltransferase, GPI-anchored to the plasma membrane; cell wall maintanance
 Resistance proteins
  AFUA_1G03200 mfsC MFS transporter
  AFUA_1G10370   MFS multidrug transporter
  AFUA_1G10390 abcB ABC multidrug transporter
  AFUA_1G13800   MFS multidrug transporter
  AFUA_3G02610   MFS transporter, has domain(s) with predicted role in transmembrane transport and integral to membrane localization
  AFUA_5G00980   MFS multidrug transporter, putative transporter of small solutes
  AFUA_5G02700   MFS multidrug transporter, putative transporter of small solutes
  AFUA_7G01790 ssu1 MFS transporter, putative sulphite efflux pump
  AFUA_2G14570   zinc/cadmium resistance protein, ortholog(s) have zinc ion transmembrane transporter activity, role in cellular zinc ion homeostasis
  AFUA_6G02220   MFS toxin efflux pump
  AFUA_8G02050   putative transporter of polysaccharides
 Heat shock, chaperone activity
  AFUA_1G07440 hsp70 molecular chaperone Hsp70
  AFUA_1G06020   DnaJ domain protein, has domain(s) with predicted heat shock protein binding, unfolded protein binding activity and role in protein folding
  AFUA_1G11180 hsp78 heat shock protein/chaperonin HSP78
  AFUA_1G15270   heat shock protein Hsp98/Hsp104/ClpA, ortholog(s) have cytosol, nuclear envelope localization
  AFUA_3G14540 hsp30 heat shock protein Hsp30/Hsp42, putative 30-kDa heat shock protein
  AFUA_4G12850 clxA calnexin, ER membrane chaperone involved in folding of glycoproteins directed to the secretory pathway
  AFUA_5G07340   DnaJ domain protein Psi, ortholog(s) have cytosol, nucleus localization, involved in protein folding and translational initiation
  AFUA_6G06470   heat shock protein Hsp30-like, putative integral plasma membrane heat shock protein
B30 up-regulation and 180 min down-regulation
 Protein/ peptide degradation and modification
  AFUA_5G06060 skpA sulfur metabolism regulator SkpA, part of SCF ubiquitin ligase complex
  AFUA_1G04040 ubiA ubiquitin
  AFUA_5G04000   protein involved in proteasomal and 4S ribosomal subunit biogenesis
 Peptidases
  AFUA_3G05450   glutamate carboxypeptidase
  AFUA_6G04510   O-sialoglycoprotein endopeptidase, ortholog(s) have chromatin DNA binding activity and role in positive regulation of transcription from RNA polymerase II promoter
  AFUA_6G07330   methionine aminopeptidase, type I, orthologs have functions in protein processing
 Glycosylation
  AFUA_6G12360   class I alpha-mannosidase 1A, has domain(s) with predicted calcium ion binding, mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
  AFUA_4G10070   class I alpha-mannosidase, has domain(s) with predicted calcium ion binding, mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
  AFUA_1G12630   mannosylphosphate transferase (Mnn4), putative phosphorylcholine metabolism
  AFUA_4G10750   alpha-1,6-mannosyltransferase subunit, Glycan biosynthesis
  AFUA_5G05740 gmtA Golgi GDP-mannose transporter, involved in biosynthesis of the cell wall polysaccharide galactomannan
 Phosphorylation
  AFUA_6G12820 mpkB MAP kinase MpkB, putative mitogen-activated protein kinase
  AFUA_5G11730   RIO1 family protein kinase, ortholog(s) have nucleocytoplasmic transporter activity, protein kinase activity, role in maturation of SSU-rRNA
  AFUA_1G12940 sakA MAP kinase SakA, nitrogen sensing, is induced upon carbon and nitrogen starvation [52]
  AFUA_1G09170   protein kinase activator (Mob2), ortholog(s) have kinase binding activity and role in conidiophore development, hyphal growth, regulation of kinase activity
  AFUA_1G16000   serine/threonine protein kinase, has domain(s) with predicted ATP binding, protein tyrosine kinase activity and role in protein phosphorylation
  AFUA_2G13680   calcium/calmodulin-dependent protein kinase, orthologs have a function in stress response
  AFUA_2G05490   HEAT repeat protein, ortholog(s) have deoxyhypusine monooxygenase activity
  AFUA_3G12490   protein arginine methyltransferase RmtB, ortholog(s) have histone-arginine N-methyltransferase activity
  AFUA_4G13400   glycosyltransferase family 28, ortholog(s) have N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity
  AFUA_5G01740   deoxyhypusine synthase, putatively first step in hypusine biosynthesis
180 min down-regulation
 ATP binding (GO:0005524)
  AFUA_1G02570   aspartyl-tRNA synthetase, cytoplasmic, aspartyl-tRNA synthetase; calcium downregulated
  AFUA_1G05620   phenylalanyl-tRNA synthetase, beta subunit, ortholog(s) have phenylalanine-tRNA ligase activity
  AFUA_1G05800 mkk2 MAP kinase kinase (Mkk2), putative mitogen-activated protein kinase kinase (MAPKK); essential for cell wall integrity signaling; calcium induced
  AFUA_1G09010   methionyl-tRNA synthetase, ortholog(s) have cytosol localization
  AFUA_1G10310   RNase L inhibitor of the ABC superfamily, ATPase, Rnase L inhibitor, orthologs involved in ribosome protection
  AFUA_1G10630   S-adenosylmethionine synthetase, putative S-adenosylmethionine synthetase; involved in methylation processes, biosynthesis of biotin and polyamines
  AFUA_2G02320   Hsp70 chaperone (BiP)
  AFUA_2G02590   aspartyl-tRNA synthetase Dps1
  AFUA_2G03580   phenylalanyl-tRNA synthetase beta chain, ortholog(s) have phenylalanine-tRNA ligase activity
  AFUA_2G04620 bipA Hsp70 chaperone BiP/Kar2
  AFUA_2G05650   cytoplasmic asparaginyl-tRNA synthetase, ortholog(s) have asparagine-tRNA ligase activity, role in asparaginyl-tRNA aminoacylation and cytosol localization
  AFUA_2G06110   chromatin remodeling and histone, ortholog(s) have role in chromatin silencing at centromere
  AFUA_2G08670   acetyl-CoA carboxylase, ortholog(s) have acetyl-CoA carboxylase activity, biotin carboxylase activity and role in long-chain fatty acid biosynthetic
  AFUA_2G09290 hsp60 antigenic mitochondrial protein HSP60, involved in heat shock response
  AFUA_2G13140 ime2 meiosis induction protein kinase, a serine/threonine protein kinase involved in mycotoxin production and sex. development
  AFUA_2G14030   arginyl-tRNA synthetase, ortholog(s) have arginine-tRNA ligase activity, role in arginyl-tRNA aminoacylation and cytosol, mitochondrion localization
  AFUA_3G05430   DEAD-box RNA helicase Dhh1/Vad1, ortholog(s) have translation regulator activity, nucleic acid binding activity
  AFUA_3G08650   C1 tetrahydrofolate synthase
  AFUA_3G10300   putative galactokinase with a role in galactose catabolism
  AFUA_3G10530   protein serine/threonine kinase (Ran1), orthologs have negative regulation of transcription/ development-meiosis
  AFUA_3G13030   t-complex protein 1, gamma subunit (Cct3), ortholog(s) have unfolded protein binding activity, role in cellular response to drug, protein folding
  AFUA_4G07660 ded1 ATP dependent RNA helicase (Dbp1), ATP-dependent RNA helicase, cell cycle affected in S. pombe
  AFUA_4G08060   tetrahydrofolylpolyglutamate synthase (Met7), role in one-carbon metabolic process, regulation of DNA methylation and cytosol, mitochondrion
  AFUA_4G13700   threonyl-tRNA synthetase, putative tRNA charging
  AFUA_5G05490   seryl-tRNA synthetase,
  AFUA_5G05960   serine/threonine protein kinase, involved in salt tolerance in S. cerevisiae
  AFUA_5G07020   ribosome biogenesis ABC transporter Arb1
  AFUA_5G09610   cysteinyl-tRNA synthetase, putative tRNA charging
  AFUA_5G10550   ATP synthase F1, beta subunit, orthologs are required for synthesis of ATP, but are non-essential
  AFUA_6G04730   bifunctional purine biosynthetic protein Ade1, ortholog(s) have phosphoribosylamine-glycine ligase activity, phosphoribosylformylglycinamidine cyclo-ligase activity
  AFUA_6G05080   ABC transporter, ortholog in S. cerevisiae involved in RNA regulation and maturation
  AFUA_6G06870   casein kinase I homolog, ortholog(s) have magnesium ion binding, protein serine/threonine kinase activity
  AFUA_6G07540   t-complex protein 1, epsilon subunit, ortholog(s) have chaperonin-containing T-complex localization
  AFUA_6G07640   lysyl-tRNA synthetase,
  AFUA_6G12630   leucyl-tRNA synthetase, putative tRNA charging
  AFUA_6G12820 mpkB MAP kinase MpkB, orthologs are regulating carbon utilization
  AFUA_7G05660   translation elongation factor eEF-3
 Transcriptional control
  AFUA_2G11780   C2H2 transcription factor (CreA) ortholog(s) have carbon catabolite repression
  AFUA_2G13260 medA transcriptional regulator of adherence, host cell interactions and virulence; required for wild-type levels of conidiation
  AFUA_2G16230   C2H2 finger domain protein, putative transcription factor, orthologs have predicted regulation of gluconeogenesis and adherence
  AFUA_2G17220   C2H2 transcription factor (AmdX), A. nidulans ortholog involved in regulation of acetamide catabolism; regulates amdS transcription
  AFUA_3G08010 ace1 C2H2 transcription factor (Ace1), involved in cation homeostasis and in response to abiotic stress in A. nidulans
  AFUA_3G10300   putative galactokinase ortholog in S. cerevisiae involved in conversion of alpha-D-galactose to galactose-1-phosphate, a key step in galactose catabolism
  AFUA_3G10530   protein serine/threonine kinase (Ran1), orthologs have negative regulation of transcription/ development-meiosis
  AFUA_3G11250 ace2 C2H2 transcription factor (Swi5), role in conidiophore development, pigment production, germination and virulence
  AFUA_4G10220   homeobox transcription factor (RfeB), ortholog(s) have role in conidiophore development, conidium formation, hyphal growth, regulation nucleotide biosynthesis
  AFUA_4G11480   C2H2 finger domain protein, S. cerevisiae ortholog is Zinc-regulated transcription facto
  AFUA_4G12470 cpcA bZIP transcriptional activator of the cross-pathway control system of amino acid biosynthesis upon starvation
  AFUA_5G06190 steA putative transcription factor involved in sexual development
  AFUA_6G02110   MADS box transcription factor Mcm1, orthologs are involved in cell cycle
 Energy
  AFUA_6G12930 acoA aconitate hydratase, is essential for energy metabolism, TCA cycle and lysine biosynthesis [59]
 Transmembrane transport GO:0055085
  AFUA_1G05020   putative sulfate transporter
  AFUA_2G03860 zrfB plasma membrane low affinity zinc ion, Low affinity plasma membrane zinc transporter; induced by zinc depletion
  AFUA_2G14570   zinc/cadmium resistance protein, ortholog(s) have zinc ion transmembrane transporter activity, role in cellular zinc ion homeostasis
  AFUA_3G12900 hasB MFS transporter, orthologous member of the “has” secondary metabolite biosynthetic gene cluster of strain A1163. [67]
  AFUA_4G14230   MFS transporter, putative transporter of small solutes
  AFUA_4G14670   MFS quinate transporter, has domain(s) with predicted substrate-specific transmembrane transporter activity
  AFUA_5G00980   MFS multidrug transporter, putative transporter of small solutes
  AFUA_5G02700   MFS multidrug transporter, putative multidrug resistant protein
  AFUA_7G01790 ssu1 MFS transporter, putative sulphite efflux pump
  AFUA_7G05220   putative mitochondrial carrier protein
  AFUA_7G05420   mitochondrial intermembrane space protein Mia40, putatively involved in intermembrane space import
180 min up-regulation
 DNA repair
  AFUA_2G02090 agt O6-alkylguanine DNA alkyltransferase; role in DNA repair
  AFUA_3G11610 nhp6 nucleosome binding protein, non-histone chromosomal protein ortholog in S. cerevisiae play role in elongation and DNA repair
 Transcription factors
  AFUA_2G15680   transcription initiation factor iia small chain, ortholog(s) have TBP-class protein binding, activity involved in preinitiation complex assembly activity
  AFUA_4G03960 farA C6 transcription factor Ctf1A, role in beta oxidation of long-chain fatty acids
  AFUA_7G06320   C6 transcription factor, has domain(s) with predicted DNA binding, sequence-specific DNA binding RNA polymerase II transcription factor activity
 Protein binding, degradation, modification
  AFUA_5G05790   ubiquitin ligase subunit HrtA, ring finger protein rbxA, putative E3 ubiquitin-protein ligase; NeddH-associated protein
  AFUA_6G09160   ubiquitin conjugating enzyme Ubc8, negatively regulates gluconeogenesis by mediating the ubiquitination of fructose-1,6-bisphosphatase [70]
  AFUA_6G14210   ubiquitin conjugating enzyme UbcB, ortholog(s) have ubiquitin-protein ligase activity
  AFUA_1G07470 atg8 autophagic death protein atg8, ribo involved in autophagy, determines the size of the autophagosome, induced upon starvation
 Systemic interaction with the environment
  AFUA_4G00660   sensor histidine kinase/response regulator, putative stress sensor
 Nitrilases/ cyanid hydratases
  AFUA_6G13450   nitrilase, ortholog(s) have cyanide hydratase activity, nitrilase activity and role in cyanide catabolic process
  AFUA_2G17500   cyanide hydratase/nitrilase, ortholog(s) have cyanide hydratase activity, nitrilase activity and role in cyanide catabolic process
 Oxidation-reduction process GO:0055114
  AFUA_2G10960 adh2 putative alcohol dehydrogenase Adh2p, in S. cerevisiae is responsible for catalyzing the initial step in the utilization of ethanol as a carbon source
  AFUA_2G11250   aryl-alcohol dehydrogenase Aad14, unknown function
  AFUA_2G15930   alcohol dehydrogenase, ortholog in S. pombe role in detoxifying alcohols and related compounds, protecting against environmental stresses
  AFUA_4G12990 trr1 thioredoxin reductase Trr1/Trr2, orthologs play a role in detoxification
 Iron homeostasis [12]
  AFUA_3G03640 mirB MFS siderochrome iron transporter MirB,
  AFUA_3G03440 mirD MFS siderophore iron transporter, expression upregulated under low iron condition
  AFUA_7G06060 sit1 siderochrome-iron transporter Sit1,
  AFUA_1G17270 fre2 FRE family ferric-chelate reductase, metalloreductase involved in response to iron starvation; reductive iron assimilation, freB
  AFUA_3G03410 sidH enoyl-CoA hydratase/isomerase family protein, mevalonyl-CoA hydratase; is essential for (TAFC) biosynthesis
  AFUA_3G03400 sidF siderophore biosynthesis acetylase AceI, hydroxyornithine transacylase; involved in extracellular siderophore biosynthesis; essential for TAFC biosynthesis
  AFUA_3G03420 sidD nonribosomal peptide synthase SidD, fusarinine C non-ribosomal peptide synthetase (NRPS) involved in extracellular siderophore biosynthesisthesis
  AFUA_3G03430 sitT ABC multidrug transporter SitT, involved in siderophore excretion
  AFUA_3G03440 mirD MFS siderophore iron transporter,
  AFUA_2G07680 sidA L-ornithine N5-oxygenase SidA, first committed step in siderophore biosynthesis; TAFC and ferricrocin biosynthesis
 Reductive iron assimilation
  AFUA_5G03790 fetC ferrooxidoreductase Fet3,; reductive iron assimilation, FetC
  AFUA_5G03800 ftrA high-affinity iron transporter FtrA, reductive iron assimilation, FtrA
 Gluconeogenesis
  AFUA_6G07720 acuF phosphoenolpyruvate carboxykinase AcuF, essential for gluconeogenesis
  AFUA_4G11310 fbp1 fructose-1,6-bisphosphatase Fbp1, essential for glucenogenesis
  AFUA_6G09160   ubiquitin conjugating enzyme Ubc8, n negatively regulates gluconeogenesis by mediating the ubiquitination of fructose-1,6-bisphosphatase [70]
  1. Adjusted categories and curated DEGs from FunCat and GO functional analysis that are refered to in the text. DEGs were manually investigated using the Aspergillus Genome Database, http://www.aspergillusgenome.org/ (ASPGD). The known description, putative function or ortholog function obtained are directly cited from ASPGD, from cited paper or description was obtained from link to S. cerevisiae genome project (http://www.yeastgenome.org/), from Candida Genome Database (http://www.candidagenome.org/), from S. pombe pombase (http://www.pombase.org/) [92], and from Neurospora crassa Sequencing Project Broad Institute of Harvard and MIT (http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html)