Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins

Abstract

In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest family. Emerging knowledge on the structure and function of PUX proteins highlights that these proteins are versatile factors for plant homeostasis and adaptation that might inspire biotechnological applications.

Targeting plant UBX proteins: AI-enhanced lessons from distant cousins

“…Instead, HsUBXN6 uses its PUB domain to recognize the C-terminal PUB-interacting motif (PIM) of p97, and it is the HsUBXN6 VCP/p97-interacting motif (VIM) that binds to p97-N (Box 1). AtPUX2 also has an atypical S3-S4 loop in its UBX domain, suggesting that it cannot bind to AtCDC48A-N [16], and AtCDC48A contains a PIM as a potential interaction partner for AtPUX2 PUB [16]. However, instead of a VIM, AtPUX2 contains a putative CDC48A-N-binding SHP box in its N-terminal.…”

“…p97 via their C-terminal SHP box and UBX domain [17], suggesting canonical CDC48/p97 associations also for the other members of these subgroups. The biological functions of SEP domains remain incompletely understood [16]. then AF is also certain about the relative position of the amino acids that form this domain.…”

“…Groups IVa and IVb contain both a short helix and a predicted second SHP motif upstream of their SEP domain [16,18]. For both subgroups, AlphaFold suggests that this helix folds back onto the SEP domain and that the helix-SHP-SEP fragment in these orthologs is, in fact, a single structural unit (Boxes 2 and 3).…”

Elevated inorganic carbon and salinity enhances photosynthesis and ATP synthesis in picoalga Picocystis salinarum as revealed by label free quantitative proteomics

“…An interesting finding is that significant group of proteins, i.e., plant ubiquitin regulatory X domain-containing proteins: Plant UBX domain-containing protein 3 (PUX3) and plant UBX domain-containing protein 4 (PUX4) were also found to be highly upregulated in M medium grown cells. These PUXs are involved in regulation of the cell division control protein 48 (CDC48) that forms the core of a multifunctional multiprotein complex that can control protein/RNA expression and extract proteins from their environment for reuse or degradation (Zhang et al, 2021). Also, another regulatory protein AtDJ1C, belonging to the DJ-1 superfamily has been found to have essential role in chloroplast development and maturation in Arabidopsis thaliana (Lin et al, 2011).…”

Arabidopsis Iron Superoxide Dismutase FSD1 Protects Against Methyl Viologen-Induced Oxidative Stress in a Copper-Dependent Manner

“…Thus, fsd1 mutants exhibited an unique upregulation of three isoforms of plant UBX domain-containing protein (PUX3, PUX11 and PUX13). They act as adaptor proteins of cell division control protein CDC48 responsible for the extraction of proteins from their environment for reuse or degradation ( Zhang et al, 2021 ). The precise function of the CDC48-PUX module during oxidative stress remains to be elucidated.…”