archaea and bacteria were also believed to synthesize lysine through diaminopimelate until it was reported that the extremely thermophilic bacterium thermus thermophilus synthesizes lysine through -aminoadipate [ 58 ] . during lysine biosynthesis in the budding yeast saccharomyces cerevisiae , -aminoadipate is synthesized from 2-oxoglutarate and acetyl - coa by the enzymes lys20 or lys21 ( homocitrate synthase [ hcs ] ) , lys4 ( homoaconitase ) , lys12 ( homoisocitrate dehydrogenase ) , and -aminoadipate aminotransferase . lysine is synthesized from -aminoadipate by the enzymes lys2 ( aminoadipate reductase ) , lys5 ( phosphopantetheinyl transferase which posttranslationally modifies lys2 ) , lys9 ( saccharopine dehydrogenase , glutamate forming ) , and lys1 ( saccharopine dehydrogenase , lysine forming ) [ 1 , 4 ] . it has been unclear why s. cerevisiae has 2 hcss ( lys20 and lys21 ) . for example , homocitrate is mainly synthesized through lys21 during growth on ethanol , while under fermentative metabolism , lys20 and lys21 play redundant roles . it was recently reported that lys20 of s. cerevisiae functions in nuclear activities involving chromatin regulation that are distinct from its previously established role in lysine synthesis . lys20 of s. cerevisiae is linked to the dna damage repair process via the histone acetyltransferase esa1 and the h2a.z histone variant . i selected 71 hcss ( 31 from saccharomycotina species , 30 from pezizomycotina species , 2 from taphrinomycotina species , and 8 from basidiomycota species ) based on blastp results in the fungal genome database at ncbi ( http://www.ncbi.nlm.nih.gov/projects/genome/guide/fungi/ ) . multiple alignments were generated with clustal w. a maximum likelihood tree was reconstructed using mega version 5 . the -distributed rate was considered , and the number of discrete gamma categories was 3 . the nucleosome position profiles were compared between the promoter ( 1000 bases upstream of the translational start site ) and coding regions ( between the translational start and end site ) of the hcs genes , according to a previously described method . similarity between the two nucleosome position profiles was estimated using the spearman 's rank correlation coefficient . the hcs phylogenetic tree ( figure 1 ) indicates that the hcs gene has been duplicated multiple times in the course of ascomycete evolution . the 31 hcss of the saccharomycotina species ( ascomycetous yeasts ) are encoded in 17 organisms . in contrast , the 30 hcss of the pezizomycotina species ( filamentous ascomycetes ) are encoded in 28 organisms . thus , 14 of the 17 saccharomycotina species and 2 of the 28 pezizomycotina species have 2 hcss ( figure 1 ) . gene duplication is not found in lys1 , lys2 , lys5 , lys9 , and their homologues . in addition , no duplication was found in lys4 , lys12 , and their homologues ( data not shown ) . therefore , among the fungal lysine biosynthesis - related genes , only the hcs gene has been duplicated . phylogenetic analysis of hcss in ascomycetous yeasts showed that the s. cerevisiae hcss ( lys20 and lys21 ) are most closely related to each other ( figure 1 ) , suggesting that hcs gene duplication occurred during evolution of the genus saccharomyces . on the other hand , all saccharomycotina species except ashbya gossypii , vanderwaltozyma polyspora , and yarrowia lipolytica have duplicated hcs genes ( figure 1 ) . thus , hcs gene duplication may be related to genome duplication events in saccharomycotina [ 1618 ] . in addition to the phylogenetic analysis based on hcs amino acid sequences , i compared the nucleosome positioning of lys20 and lys21 . interestingly , nucleosomes were mapped to the hcs gene promoters more often than to the coding regions ( figure 2 ) . nucleosome position profiles in the coding regions were highly correlated ( spearman 's rank correlation coefficient = 0.833 ) between lys20 and lys21 . on the other hand , those in the gene promoter regions were poorly correlated ( spearman 's rank correlation coefficient = 0.396 ) . this result suggests that these 2 hcs genes have different regulatory systems . on the other hand , lys20 expression is most similar to lys21 expression , and lys21 is most similar to lys20 expression , based on the spell version 2.0.2 . in addition , recent comparative analyses of orthologous genes in evolutionarily close yeasts indicated that divergence of nucleosome positioning is not correlated with divergence of gene expression [ 20 , 21 ] . although hcs ( lys20 and lys21 ) is located in the nucleus of s. cerevisiae , hcs is located in the cytoplasm of penicillium chrysogenum [ 23 , 24 ] . the phylogenetic tree ( figure 1 ) showed that gene duplication is not found in basidiomycota and taphrinomycotina . in addition , gene duplication has occurred rarely in pezizomycotina , suggesting that a common ancestor of the dikarya lacked the nuclear function of chromatin regulation . considering that duplication of the hcs gene occurred in a limited number of ascomycetes , it may not be an essential event in the evolution of dikarya . i hypothesize that after divergence of the phyla ascomycota and basidiomycota , s. cerevisiae obtained hcs bifunctionality .