Structure–function analysis of Knr4/Smi1, a newly member of intrinsically disordered proteins family, indispensable in the absence of a functional PKC1–SLT2 pathway in Saccharomyces cerevisiae

Abstract

The coordination between cell wall synthesis and cell growth in the yeast Saccharomyces cerevisiae implicates the PKC1-dependent MAP kinase pathway. KNR4, encoding a 505 amino acid long protein, participates in this coordination, since it displays synthetic lethality with all the members of the PKC1 pathway and shows physical interaction with Slt2/Mpk1. The recent finding that KNR4 interacts genetically or physically with more than 100 partners implicated in different cellular processes raised the question of how these interactions may occur and their physiological significance. This called for an in-depth structure-function analysis of the Knr4 protein, which is reported in the present paper. Computational analysis supported by biochemical and biophysical data characterize Knr4 as a newly identified member of the growing family of intrinsically disordered proteins. Despite disordered regions that are located at the N-and C-termini and are probably responsible for fine regulatory function; this protein contains a structured central core (amino acid residues 80-340) that is able to restore wild-type phenotypes of knr4 mutant in stress conditions. However, this fragment was unable to complement synthetic lethality between knr4 mutations and deletions of genes encoding protein kinases of the PKC1-dependent pathway. For these crucial events to occur, the presence of the Nterminal part of Knr4 protein is indispensable. Moreover, we demonstrate that this protein is essential for cell viability in the absence of a functional Pkc1-Slt2 pathway, since the lethality caused by KNR4 deletion in such a genetic background could not be compensated by overexpression of any gene from yeast genomic libraries.

Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes

“…Instead, it shares high sequence similarity with proteins of Aeromonas salmonicida (53% amino-acid identity, Table 1) and various Bacillus species (including B. thuringiensis , B. cereus , and B. weihenstephanensis , 42–49% identity, see alignment in Supplementary Figure S1A). None of these proteins is annotated, except the B. cereus protein annotated as a member of the SMI1/KNR4 family, involved in the regulation of the cell wall synthesis in yeast [28]. The SMI1 protein of S. cerevisiae ( YGR229C ) has homologs in all hemiascomycetous yeasts, including K. lactis (KLLA0E15775p protein) but those are 3- to 4-fold longer in sequences than KLLA0B05269g and share only limited sequence identity with it (average 22%, Table 1).…”

The resistance of the yeast Saccharomyces cerevisiae to the biocide polyhexamethylene biguanide: involvement of cell wall integrity pathway and emerging role for YAP1

“…Mutation of the SMI1/KNR4 gene increased the sensitivity of the yeast cells to PHMB (Figure 2). It was recommended that Smi1p/Knr4p should coordinate the cell cycle progression in connection with cell wall synthesis and this protein was shown to be essential for viability of the cell in the absence of a functional PKC1/Slt2 pathway [35]. A physical interaction between Knr4p and Slt2p was also described and it was proposed that such interaction modulate the Slt2p-dependent activation of Rlm1 and SBF transcriptional factors [36].…”

Protein Flexibility and Coiled-Coil Propensity: New Insights Into Type III and Other Bacterial Secretion Systems

“…proteins, membranes, nucleic acids and small molecules (Durand et al, 2008;Uversky et al, 2009). Because of their functional importance, intrinsically disordered domains are very common in proteomes and play crucial roles in signaling, recognition, regulation and self-assembly (Namba, 2001).…”