Protein Prenylation in Plants: Mechanisms and Functional Implications

Abstract

Protein prenylation is a crucial post-translational modification that involves the formation of a covalent bond between isoprenoid lipids and the cysteine residues of specific proteins. This modification plays a significant role in determining protein localization, facilitating protein-protein interactions, and ultimately influencing protein function within the cellular context. Prenylation is a conserved process observed across various kingdoms of life, including plants, animals, fungi, and protists. This review aims to consolidate existing knowledge regarding the mechanisms underlying protein prenylation, encompassing the biosynthetic pathways of isoprenoids in plants and the processing involved in the prenylation modification. Furthermore, it highlights the implications of alterations in protein prenylation on plant development, signaling pathways, and stress responses. The review also addresses the similarities in modification mechanisms between plants and animals, as well as the diversity of their functional implications. Finally, it outlines prospective research directions of the plant prenylation mechanisms and the potential applications in the field of biotechnology.

Keywords: farnesyltransferase; functional implications; geranylgeranyltransferase; modification mechanism; protein prenylation.

Figure 1

Phylogenetic relationships of prenyltransferase proteins. The full-length amino sequences of prenyltransferase proteins from monocotyledons and dicotyledons plants were used for evolutionary analyses. Monocotyledons: Oryza sativa (Os), Hordeum vulgare (Hv), Zizania palustris (Zp), Zizania latifolia (Zl), Panicum hallii (Ph), Setaria italica (Si), Miscanthus floridulus (Mf), Brachypodium distachyon (Bd), Triticum urartu (Tu), Triticum dicoccoides (Td), Aegilops tauschii subsp. strangulate (Aet), Phragmites australis (Pa), Alopecurus aequalis (Aa), Triticum aestivum (Ta). Dicotyledons: Arabidopsis thaliana (At), Camelina sativa (Cs), Capsella rubella (Cr), Eutrema salsugineum (Es), Cardamine amara subsp. amara (Ca), Raphanus sativus (Rs), Brassica carinata (Bc), Brassica rapa (Br), Brassica napus, Tarenaya hassleriana (Th), Gossypium hirsutum (Gh), Arachis hypogaea (Ah), Medicago truncatula (Met), Glycine max (Gm). These analyses were performed in MEGA7 using the Neighbor-Joining method, with the bootstrap value set to 1000 [10]. Evolutionary distances were calculated using the JTT matrix-based method. In the phylogenetic tree, monocotyledonous plants are highlighted in red font, while dicotyledonous plants are indicated in black font. The evolutionary analysis clearly classified these proteins into five distinct groups, each group displayed with a different colored background.

Figure 2

Predicted schematic structures of plant prenyltransferase proteins. The full-length amino acid sequences of prenyltransferase proteins (as shown in Figure 1) were used. In the left section of the figure, the homology analysis of these proteins is displayed. These analyses were performed using the DNAMAN program with the full-length amino acid sequences. The middle section presents the conserved domains identified through the MEME tool [11]. For each protein, the actual motif length and order are indicated. The right section illustrates the motif symbols along with the corresponding consensus sequences for each domain. Sequence LOGOs for each protein domain motif were generated using the MEME algorithm. The height of individual letters within the stack reflects their probability of occurrence at that specific position, multiplied by the total information content of the stack.

Figure 3

Protein Prenylation in Plants. The figure depicts the structure of CAAX protein prenyltransferases (including FTase and GTase), their substrate preference for a C-terminal motif, the processing steps of prenylated protein modification, and the final form of the prenylated substrate.

Figure 4

Structural overview of prenyltransferase heterodimers. Farnesyltransferase (FTase) (PDB ID: 1S63), geranylgeranyltransferase I (GGTase-I) (PDB ID: 1N4R), GGTase-II (PDB ID: 3DSV), and GGTase-III (PDB ID: 6O60). The α subunits are rendered in green color gradients, while β subunits are presented in orange gradients. Each subpanel is divided into three sections: the helical structure in cartoon representation, molecular surface, and magnified views of the binding pockets. All heterodimers display Zn²⁺ coordination, with additional Ca²⁺ coordination observed specifically in the GGTase-II polymer. Key molecular components—including Zn²⁺ ions, farnesyldiphosphate (FPP), and the prenylated peptide—are explicitly indicated by arrows within their respective binding pockets.