LDIP cooperates with SEIPIN and LDAP to facilitate lipid droplet biogenesis in Arabidopsis

Abstract

Cytoplasmic lipid droplets (LDs) are evolutionarily conserved organelles that store neutral lipids and play critical roles in plant growth, development and stress responses. However, the molecular mechanisms underlying their biogenesis at the endoplasmic reticulum (ER) remain obscure. Here we show that a recently identified protein termed LDIP (LD-Associated Protein [LDAP]-Interacting Protein) works together with both endoplasmic reticulum-localized SEIPIN and the LD-coat protein LDAP to facilitate LD formation in Arabidopsis thaliana. Heterologous expression in insect cells demonstrated that LDAP is required for the targeting of LDIP to the LD surface, and both proteins are required for the production of normal numbers and sizes of LDs in plant cells. LDIP also interacts with SEIPIN via a conserved hydrophobic helix in SEIPIN and LDIP functions together with SEIPIN to modulate LD numbers and sizes in plants. Further, co-expression of both proteins is required to restore normal LD production in SEIPIN-deficient yeast cells. These data, combined with the analogous function of LDIP to a mammalian protein called LD Assembly Factor 1, are discussed in the context of a new model for LD biogenesis in plant cells with evolutionary connections to LD biogenesis in other eukaryotes.

Finding new friends and revisiting old ones – how plant lipid droplets connect with other subcellular structures

“…Notably, in the last few years, many new LD proteins have been discovered that are directly involved in LD biogenesis, function, and/or breakdown (Horn et al ., 2013; Pyc et al ., 2017, 2021; Fernandez‐Santos et al ., 2020; Kretzschmar et al ., 2020). Some of these proteins have been also implicated in mediating the physical connections that exist between LDs and other subcellular structures (Greer et al ., 2020; Pyc et al ., 2021; Krawczyk et al ., 2022b). These connections are defined as membrane contact sites (MCSs) if the following conditions are fulfilled: (1) a connection of organelles mediated by tethering proteins, (2) no fusion of the organelles, (3) the fulfillment of a specific function(s) by the MCS, and (4) the presence of a defined proteome at the MCS (Scorrano et al ., 2019).…”

“…Furthermore, various proteins are integrated into the LD monolayer, some of which are thought to extend into the hydrophobic core (Huang, 2018), while others appear to be attached directly to the LD surface (Gidda et al ., 2016) or through protein–protein interactions (Krawczyk et al ., 2022b). Notably, in the last few years, many new LD proteins have been discovered that are directly involved in LD biogenesis, function, and/or breakdown (Horn et al ., 2013; Pyc et al ., 2017, 2021; Fernandez‐Santos et al ., 2020; Kretzschmar et al ., 2020). Some of these proteins have been also implicated in mediating the physical connections that exist between LDs and other subcellular structures (Greer et al ., 2020; Pyc et al ., 2021; Krawczyk et al ., 2022b).…”

“…In Arabidopsis, LIPID DROPLET‐ASSOCIATED PROTEIN 1, 2 and 3 (LDAP 1, 2 and 3) and their interaction partner LDAP‐INTERACTING PROTEIN (LDIP) also bind to nascent LDs (Coulon et al ., 2020; Pyc et al ., 2021). LDIP additionally interacts with at least SEIPIN1 and SEIPIN2 and appears to function with them at the LD‐ER junction (Pyc et al ., 2021).…”

“…In Arabidopsis, LIPID DROPLET‐ASSOCIATED PROTEIN 1, 2 and 3 (LDAP 1, 2 and 3) and their interaction partner LDAP‐INTERACTING PROTEIN (LDIP) also bind to nascent LDs (Coulon et al ., 2020; Pyc et al ., 2021). LDIP additionally interacts with at least SEIPIN1 and SEIPIN2 and appears to function with them at the LD‐ER junction (Pyc et al ., 2021). Hidden Markov model searches revealed that the LDAPs and LDIP have homology with the human perilipin proteins (Box 1), and lipid droplet assembly factor 1 (LDAF1), respectively (Pyc et al ., 2021).…”

“…LDIP additionally interacts with at least SEIPIN1 and SEIPIN2 and appears to function with them at the LD‐ER junction (Pyc et al ., 2021). Hidden Markov model searches revealed that the LDAPs and LDIP have homology with the human perilipin proteins (Box 1), and lipid droplet assembly factor 1 (LDAF1), respectively (Pyc et al ., 2021). While perilipin proteins are generally considered LD surface‐associated proteins with numerous functions (Itabe et al ., 2017), LDAF1 forms an oligomeric complex in a 1 : 1 stoichiometry with seipin proteins during LD initiation in mammalian cells, and might additionally coat the nascent LD (Chung et al ., 2019), a model that could also be considered analogous for the SEIPIN–LDIP complex.…”