Researchers uncover how an enzyme helps a sundew digest its victim's DNA

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In a study published in the Annals of Botany, researchers have delved into the inner workings of the Lance-leaved sundew, Drosera adelae, a carnivorous plant known for its unique trap organ and digestive system. The research, by Meng Yu and colleagues in Japan, uncovered new information about a specialized enzyme called S1-type nuclease (DAN1) in the plant’s digestive fluid. The findings reveal insights into this enzyme’s gene expression, structural characteristics, and evolutionary adaptations, which play a crucial role in the plant’s ability to absorb nutrients from its prey.

Carnivorous plants, like the Lance-leaved sundew, have evolved to trap and digest insects and other small animals to supplement their nutrient intake, particularly in nutrient-poor environments. These plants secrete digestive fluids that contain various enzymes, which break down the prey into simpler compounds. While previous studies have focused on other enzymes present in the digestive fluids of these plants, little research has been conducted on nucleases – enzymes that help break down nucleic acids like DNA and RNA.

In this study, Yu and colleagues focused on the DAN1 enzyme, an S1-type nuclease, found in the digestive fluid of Drosera adelae. They aimed to understand its gene expression, structural, functional, and evolutionary characteristics, as well as its role in the plant’s unique trap organ and associated epigenetic regulation. Epigenetic regulation refers to changes in gene activity that do not involve alterations to the underlying DNA sequence but can still be passed down through generations.

Parts of *Drosera adelae* examined in the study. Image: Yu *et al*. 2023.

The team used real-time PCR to examine the organ-specific expression of the Dan1 gene in the Lance-leaved sundew, including the glandular tentacles, laminas, roots, and inflorescences. This technique allows for the detection and quantification of specific DNA sequences. They also investigated the methylation status of the Dan1 promoter – a region of DNA that controls gene activity – by bisulfite sequencing, which reveals the extent of DNA methylation in a given sequence.

The results showed that Dan1 is exclusively expressed in the glandular tentacles, and its promoter is almost entirely unmethylated in all organs. This finding contrasts with the S-like RNase gene da-I of Drosera adelae, which has similar organ-specific expression but is controlled by a promoter that is specifically unmethylated in the glandular tentacles. This suggests that the two genes are regulated differently.

In addition to analyzing the gene expression and regulation, the researchers also studied the structural characteristics of DAN1 by comparing the primary structures of S1-type nucleases from three carnivorous and seven non-carnivorous plants. This comparison revealed seven amino acid positions conserved only among carnivorous plants and three conserved only among non-carnivorous plants. This finding indicates that evolution has shaped the structure of DAN1 to serve specific functions in the digestive fluid of carnivorous plants.

DAN1 was prepared using a cell-free protein synthesis system to understand the enzyme’s function further. Researchers then tested the enzyme’s requirements for metal ions, optimum pH and temperature, and substrate preference. They discovered that DAN1 prefers RNA over DNA as a substrate in the presence of Zn2+, Mn2+, or Ca2+ ions, and functions best at a pH of 4.0.

Based on these findings, the researchers concluded that the primary function of DAN1 in Drosera adelae is to facilitate the uptake of phosphates from the prey. This function differs significantly from the known roles of S1-type nucleases in other plants. In their article Yu and colleagues write:

Plant S1-type nucleases have roles in many biological processes, including endosperm degeneration (Brown and Ho, 1986), tracheary element differentiation (Ito and Fukuda, 2002), leaf senescence (Pérez-Amador et al., 2000) and response to viroid infection (Matoušek et al., 2007, 2008). Other than the viroid infection response, these phenomena accompany programmed cell death (PCD) (Sugiyama et al., 2000). However, studies of digestive enzymes of carnivorous plants, including the current study, suggest that S1-type nucleases are also used to digest nucleic acids of the prey, which is not associated with PCD. Furthermore, given that Dr. adelae DA-I is an S-like RNase that is abundantly present in the digestive fluid, and DAN1 seems to prefer ssRNA over ssDNA as a substrate…, Dr. adelae may obtain phosphates mainly from RNA. This may be a common feature of carnivorous plants because S-like RNases are widely found in digestive fluids of these plants…
Yu et al. 2023.