Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions

Abstract

Calpains are cysteine proteases that control cell fate transitions. Although calpains are viewed as modulatory proteases displaying severe, pleiotropic phenotypes in eukaryotes, human calpain targets are also directed to the N-end rule degradatory pathway. Several of these destabilized targets are transcription factors, hinting at a gene regulatory role. Here, we analyze the gene regulatory networks of Physcomitrium patens and characterize the regulons that are deregulated in DEK1 calpain mutants. Predicted cleavage patterns of regulatory hierarchies in the five DEK1-controlled subnetworks are consistent with the gene's pleiotropy and the regulatory role in cell fate transitions targeting a broad spectrum of functions. Network structure suggests DEK1-gated sequential transition between cell fates in 2D to 3D development. We anticipate that both our method combining phenotyping, transcriptomics and data science to dissect phenotypic traits and our model explaining the calpain's role as a switch gatekeeping cell fate transitions will inform biology beyond plant development.

CLAVATA modulates auxin homeostasis and transport to regulate stem cell identity and plant shape in a moss

“…An altered auxin distribution in the tip cells of Pprpk2 mutants or subapical cells of Ppclv1a1b mutants would support our hypothesis. An alternative hypothesis is that PpCLV1a and PpCLV1b could act at least partially independently of PpRPK2 , contributing to observed differences in mutant phenotypes between Ppcvl1a1b and Pprpk2 mutants, and there is some support for this hypothesis in recently published work (Cammarata et al ., 2021 ; Demko et al ., 2021 ).…”

Membrane-anchored calpains – hidden regulators of growth and development beyond plants?

“…The DEK1 and NOT1 are epistatic, where DEK1 is a negative regulator of NOT1, which is a negative regulator of aleurone cell fate ( Yi et al., 2011b ). Multiple transcriptional regulators have been predicted as potential DEK1 calpain substrates by ( Demko et al., 2021 ) based on P. patens gene regulatory network analysis. The ultimate confirmation of the putative DEK1 targets as genuine in vivo substrates of the calpain requires additional experimental validation.…”

How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants

“…Furthermore, PpDEK1 is able to rescue Arabidopsis dek1 mutant phenotypes ( Liang et al, 2013 ). Based on network analyses of transcriptomic data, it has been inferred that PpDEK1, which is localized to the plasma membrane in recently divided cells ( Perroud et al, 2020 ), functions as a developmental “gatekeeper” of cell fate transitions ( Demko et al, 2021 ). In the case of the transition to 3D growth during gametophyte development, PpDEK1 appears to function partly through repression of APB genes ( Demko et al, 2014 ).…”