A new study has revealed how the plant-specific KCS6-CER2 enzyme complex catalyzes very-long-chain fatty acid (VLCFA) elongation and identified a previously unknown acyl-CoA-binding cavity, shedding light on the molecular innovations that enabled plants to adapt to terrestrial environments.

Led by the Guangzhou Institutes of Biomedicine and Health (GIBH) of the Chinese Academy of Sciences (CAS) together with collaborators, this study published in Molecular Plant on July 9 provides the first complete structural reconstruction of the condensation reaction underlying plant VLCFA elongation.

VLCFAs are essential components of membrane lipids, sphingolipids, suberin, and cuticular waxes. They play critical roles in reducing water loss, protecting plants against pathogen invasion, and enabling adaptation to terrestrial environments. VLCFAs also serve as valuable renewable feedstocks for pharmaceuticals, cosmetics, lubricants, and other bio-based products.

In plants, VLCFAs are synthesized by the endoplasmic reticulum-localized fatty acid elongase (FAE) complex through iterative two-carbon elongation cycles. The initial condensation reaction, catalyzed by β-ketoacyl-CoA synthase (KCS), is both the rate-limiting and chain-length-determining step of the pathway. Unlike animals and fungi, which rely on elongases, plants have evolved a distinct elongation system in which KCS cooperates with ECERIFERUM2 (CER2) proteins. However, the molecular basis of this process remains unresolved.

Selaginella moellendorffii, an early-diverging extant vascular land plant, represents one of the earliest known lineages to possess the cooperative KCS6-CER2 elongation module. It therefore provides an important system for elucidating the mechanism of the plant-specific VLCFA elongation machinery, and also serves as a valuable evolutionary model for tracing the emergence and evolution of this system during the early colonization of land by plants.

Using S. moellendorffii as a model, the researchers determined a series of cryo-electron microscopy (cryo-EM) structures spanning the complete condensation reaction catalyzed by the KCS6-CER2 complex. These structures captured the apo state, a C22:0 acyl-enzyme intermediate, the malonyl-CoA-bound state, and the C24:0 β-ketoacyl-CoA product-bound state. Together, these structures reveal the complete sequence of molecular events underlying substrate recognition, acyl-chain loading, two-carbon condensation, and product formation.

The study also identified a previously unrecognized lateral acyl-CoA-binding cavity adjacent to the catalytic tunnel. The researchers captured a C22:0 acyl-CoA molecule within this cavity, and complementary functional analyses showed that the cavity is essential for efficient VLCFA biosynthesis. This finding expands the current understanding of substrate handling by revealing an additional acyl-CoA-binding site that may facilitate substrate processing during successive elongation cycles.

Comparative structural and phylogenetic analyses further showed that both the cooperative catalytic mechanism and the key structural features of the KCS6-CER2 complex are highly conserved across vascular plants. These results suggest that the KCS6-CER2-mediated VLCFA elongation module emerged early during land plant evolution and has been retained throughout vascular plant diversification.

Schematic illustration of the molecular mechanism by which the KCS6-CER2 enzyme complex catalyzes VLCFA elongation in plants. (Image by GIBH)

By revealing the complete structural basis of plant-specific VLCFA elongation and identifying a previously unknown acyl-CoA-binding cavity, this work deepens understanding of plant lipid metabolism, according to the researchers.

They added that the study provides new insights into the molecular innovations that supported plant adaptation to terrestrial environments and establishes a structural foundation for engineering plant wax biosynthesis, improving drought and stress tolerance, and developing high-value plant-derived lipid products.

The study was jointly led by Prof. WANG Qianmin of GIBH, Prof. CHENG Yunjiang of Huazhong Agricultural University, and Prof. XU Youwei of Guangzhou Medical University. Dr. WANG Yang of GIBH and Dr. WANG Haiyan of Huazhong Agricultural University are co-first authors. Prof. DENG Xiuxin of Huazhong Agricultural University provided important guidance. Cryo-EM data collection was supported by the Shanghai Institute of Materia Medica of CAS.

This work was supported by the Key International (Regional) Joint Research Program of the National Natural Science Foundation of China, the Foundation of Hubei Hongshan Laboratory, and the China Agriculture Research System of MOF and MARA.