Figure 1: A stereo light micrograph of a zebrafish embryo. RIKEN researchers have determined the gene that encodes for an enzyme found in zebrafish embryos. © ARTHUR CHIEN/SCIENCE PHOTO LIBRARY
RIKEN researchers have determined the molecular structure of an enzyme that occurs in fish1. This could shed light on molecular processes in a wide range of marine organisms.
Glycans are complex sugar molecules, and they play key roles in a wide range of biochemical processes. Glycans can be added to proteins by a process known as glycosylation, which is important for many biological processes including quality control of proteins, cell differentiation and immune responses.
Enzymes known as peptide:N-glycanases (PNGases) have the opposite effect and remove glycans from proteins. PNGases were first found in bacteria and plants. Subsequently, they were found in various animals.
The first example of PNGase in animals was found in the eggs and embryos of medaka fish. It was later found that fish have two types of PNGases: the one found in embryos, which is active at acidic pHs, and the other found at relatively constant levels during all stages of a fish's lifecycle, which is active at neutral pHs.
The vast majority of the research conducted to date has focused on the neutral PNGase, since it corresponds to PNGase in humans and other mammals (called NGLY1). In contrast, acid PNGase has been neglected since it is only found in fish embryos.
"As acid PNGase appears to be fish specific, not much attention has been paid to this enzyme," notes Tadashi Suzuki of the RIKEN Glycometabolic Biochemistry Laboratory. "But we believe that to understand the biology of fish, we have to dig deeper into fish-specific events."
Suzuki and Akinobu Honda, also of the Laboratory, and their co-workers set out to address this imbalance in regard to PNGase.
For the first time, they have identified the gene that encodes for acid PNGase, which they named ngly2. They also used cryo-electron microscopy to determine the molecular structure of acid PNGase.
The team used the structural features of Ngly2 to design new biochemical experiments. "Formulating hypotheses from structural information and testing them experimentally was particularly fascinating," says Honda. "I was especially excited when the experimental results were consistent with the hypotheses we proposed."
Surprisingly, knocking out ngly2 from zebrafish didn't appear to have much of an effect on embryos. "We have a sneaking suspicion that it may have been difficult to see much of an effect because zebrafish are freshwater fish," says Honda. "But knocking out ngly2 in saltwater fish may have more serious consequences."
The results may have implications for marine species beyond fish. "Since ngly2 is conserved across a broad range of aquatic organisms, including octopuses, ascidians, sea urchins, corals and shellfish, our observations suggest that this gene may play a role in adaptation to aquatic environments," says Suzuki.
