Evolution of the System of Coordinate Regulation of Proteasomal Gene Expression in the Yeast Class Saccharomycetes

The 26S proteasome is a multisubunit ATP-dependent protease complex and is necessary for the normal function of the eukaryotic cell and its survival in stress. Twenty years ago, we, in collaboration with German researchers, were the first to experimentally describe a system for coordinated regulation of proteasomal gene expression in the yeast Saccharomyces cerevisiae . This system consists of the ScRpn4 transcription factor and its binding site, called PACE. Based on the results of a bioinformatics search in the first sequenced yeast genomes, Rpn4-like proteins and PACE-like elements were postulated for other species of the class Saccharomycetes. We experimentally characterized Rpn4-like proteins in the biotechnologically significant yeast species Komagataella pfaffii ( Pichia pastoris ), Yarrowia lipolytica, and Debaryomyces hansenii and the opportunistic yeast Candida glabrata . As ample information accumulates for the genome sequences of new yeast species and strains, the question arises as to how diverse the regulatory system of proteasomal genes is in terms of structure and likely mechanisms of function. In this work, a bioinformatics search for Rpn4-like proteins and PACE-like elements was conducted in 3111 strains belonging to 427 yeast species of the class Saccharomycetes. It was shown that only the DNA-binding domain is conserved among Rpn4-like proteins, in accordance with conservation of PACE elements. Certain systems were found to contain more than one Rpn4-like protein with structural differences in the DNA-binding domain or to include an autoregulation of the genes for Rpn4-like proteins. Given that Rpn4-like proteins and proteasomes play a role in the cell response to stress, the diversity of systems for the regulation of proteasomal genes was assumed to corresponds to adaptation of organisms to their living environments.