Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens

Abstract

Phosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora. In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution. .

Autophagy modulates apical growth and development in the moss Physcomitrium patens

“…Expression data for protonemata specifically (Agudelo-Romero et al ., 2020; Xiao et al ., 2011) indicated that levels of most ATG genes are higher in caulonemata grown in optimal conditions (Fig. S8B).…”

A plant‐unique ESCRT component, FYVE4, regulates multivesicular endosome biogenesis and plant growth

“…S2c). According to the phylogenetic analysis of FYVE domain‐containing proteins, FYVE4 seems to be a plant‐specific protein with putative homologues found only in plants, but not in yeast and animals (van Leeuwen et al ., 2004; Agudelo‐Romero et al ., 2020). A Blast search in 27 plant genomes representing all major evolutionary lineages of land plants (Phytozome 11; http://www.phytozome.jgi.doe.gov) indicated that putative homologues of Arabidopsis FYVE4 protein were present in all land plants, including the early‐divergent land plant Marchantia polymorpha (liverworts) (Fig.…”

Attracted to membranes: lipid-binding domains in plants

“…Arabidopsis contains 11 PX proteins ( van Leeuwen et al, 2004;Agudelo-Romero et al, 2020; Figure 4 ). These include six Sorting Nexin proteins (SNX1, SNX2a, SNX2b, and SNX3-5), two phospholipase Ds (PLDf1 and 2), and three EREX (Endosomal Rab Effector with PX domain; EREX, EREL1, and EREL2) proteins (see Supplemental Text T2).…”

“…The PI3P-binding pocket is formed by the conserved WxxD, (R/K)(R/K)HHCR, and RVC motifs at the end of the b1-strand, whereby the lipid's head group ends up parallel to the b1 strand. Due to its small size, PPI specificity is mostly indirect, with only PI3P or PI5P fitting inside the FYVE pocket, with PI3P being preferred (Kutateladze and Overduin, 2001;Agudelo-Romero et al, 2020). Membrane localization is further positively influenced by coincidence detection, either via homodimerization, additional lipid-binding motifs, or protein-protein interaction (Lystad and Simonsen, 2016).…”

“…Arabidopsis has 15 proteins with a FYVE domain. They all contain the conserved Wxx(D/G), (R/K)(R/K)H(H/N)C(R/Y), and RVC motifs (Supplemental Figure S2; van Leeuwen et al, 2004;Wywial and Singh, 2010;Agudelo-Romero et al, 2020). Lipid binding was analyzed for four of them, including FREE1/FYVE1, a protein that is involved in complex regulation in endosomal trafficking, autophagy, and vacuolar biogenesis as well as ABA signaling and indeed binds PI3P (Barberon et al, 2014;Gao et al, 2014;Kolb et al, 2015;Garcia-Leon et al, 2019;Zhao et al, 2019).…”