Genome-Wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

Abstract

Remorins were discovered in a screen for plasma membrane (PM) proteins differentially phosphorylated in the presence of oligogalacturonides (Farmer et al., 1989). The first remorin was initially designated as pp34, as it corresponded to a phosphorylated protein with a molecular mass of 34 kD in purified PM preparations from potato (Solanum tuberosum; Jacinto et al., 1993). After a section in J.L. Borge's “Book of Imaginary Beings,” in which the remora fish is described to attach itself to larger fish and ships, this protein was renamed remorin (Reymond et al., 1996) due to its hydrophilic profile and its ability to attach to PMs (E. Farmer, personal communication). Several proteomic approaches on PM preparations from tobacco (Nicotiana tabacum) leaves and Arabidopsis (Arabidopsis thaliana) seedlings now suggest localization of remorins in association with PMs (Watson et al., 2003; Marmagne et al., 2004; Mongrand et al., 2004; Sazuka et al., 2004; Nelson et al., 2006; Valot et al., 2006). Interestingly, remorins have also been found in detergent-resistant membrane fractions, called lipid rafts (Mongrand et al., 2004; Shahollari et al., 2004; Bhat and Panstruga, 2005; Laloi et al., 2007; Lefebvre et al., 2007). Lipid rafts are characterized by an enrichment of sterols, sphingolipids, and steryl-glycosides, and are believed to be functional microdomains in PMs (Peskan et al., 2000; Mongrand et al., 2004; Borner et al., 2005; Laloi et al., 2007). Most recently, Lefebvre and coworkers demonstrated the presence of remorins in lipid raft fractions from root PMs of the model legume Medicago truncatula (Lefebvre et al., 2007). While little is known about the function of these microdomains in plants, key signaling processes during HIV-1 infection (Manes et al., 2000; Ono and Freed, 2001), spreading of malarial parasites and the Newcastle disease virus, as well as prion conversion occur at lipid rafts in mammalian systems (Samuel et al., 2001; Nishina et al., 2004; Laliberte et al., 2006). Some remorins share physical properties with viral movement proteins due to their hydrophobic N-terminal region. The C-terminal domain is generally predicted to consist of coiled-coil domains, a feature that appears to be common to all remorin proteins. This region was found to be responsible for the ability of remorins to form oligomeric filamentous structures in vitro, suggesting that these proteins might be structural components of plant cytoskeletons and/or the membrane skeletons (Bariola et al., 2004). In addition, expression of a remorin from tomato (Solanum lycopersicum) was observed in embryonic, apical, and vascular tissue (Bariola et al., 2004). However, astonishingly, there is no published genetic evidence in any plant species that can help us to decipher putative functions of remorins. The few reported attempts to generate plant mutants in which one or more of the ubiquitously expressed remorin genes were knocked out either failed or did not lead to an obvious phenotype (Reymond et al., 1996; Bariola et al., 2004). Searches in databases of fully sequenced plant species revealed the existence of eight, 16, and 19 remorin genes in Populus trichocarpa, Arabidopsis, and rice (Oryza sativa), respectively (Supplemental Table S1). Patterns of differentially regulated remorin genes and proteins have been reported in an increasing number of transcriptomic and proteomic studies. Since many of these are annotated as “unknown function,” they need to be properly classified and given suitable nomenclature. Here, we report on a genome-wide survey of the remorin family throughout fully sequenced plant genomes. We combined a phylogenetic approach with various in silico sequence-scanning tools (alignments, and motif and domain predictions) and analysis of available genetic and genomic data to identify a specific remorin signature and to define several groups within the remorin family. We used this classification to propose a general nomenclature for remorins that should help to differentiate between the different members in future studies. Keyword and BLAST searches among available data allowed us to retrieve approximately 1,000 remorin sequences corresponding to more than 130 remorin proteins from 55 different plant species (Supplemental Table S1). Importantly, no significant hits were identified among sequence data from other kingdoms (fungi, animals, archaeabacteria, and eubacteria). Unexpectedly, no remorin genes were found in algae (neither by BLAST against publicly available data nor in the Ectocarpus siliculosus full-genome sequence; M. Cock, personal communication), while remorins were identified in mosses and ferns. Canonical remorins, such as StREM (Reymond et al., 1996; now StREM1.3), are characterized by the presence of an N-terminal and a C-terminal PFAM domain (Remorin_N: PF03766; Remorin_C: PF03763). Higher sequence variability in N-terminal regions of remorins suggests structural and functional divergence and indicates tha