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Ji, Yuxuan, Wei, Li, Da, Anqi, Stark, Holger, Hagedoorn, Peter-Leon, Ciofi-Baffoni, Simone, Cowley, Sally A., Louro, Ricardo O., Todorovic, Smilja, Mroginski, Maria Andrea, Nicolet, Yvain, Roessler, Maxie M., Le Brun, Nick E. 
ORCID: https://orcid.org/0000-0001-9780-4061, Piccioli, Mario, James, William S., Hagen, Wilfred R. and Ebrahimi, Kourosh H.
(2022)
Radical-SAM dependent nucleotide dehydratase (SAND), rectification of the names of an ancient iron-sulfur enzyme using NC-IUBMB recommendations.
Frontiers in Molecular Biosciences, 9.
ISSN 2296-889X
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Abstract
In 1789, the influential French chemist Antoine-Laurent Lavoisier described his view of science and its langague in his book Traité élémentaire de chimie. According to the Robert Kerr’s translation it states (Lavoisier, 1790): “As ideas are preserved and communicated by means of words, it necessarily follows that we cannot improve the language of any science without at the same time improving the science itself; neither can we, on the other hand, improve a science without improving the language or nomenclature which belongs to it.” This view reminds us of Confucius’s earlier doctrine, the rectification of names (Steinkraus, 1980; Lau, 2000). Confucius believed that rectification of names is imperative. He explained (Steinkraus, 1980; Lau, 2000): “If language is incorrect, then what is said does not concord with what was meant, what is to be done cannot be affected. If what is to be done cannot be affected, then rites and music will not flourish. If rites and music do not flourish, then mutilations and lesser punishments will go astray. And if mutilations and lesser punishments go astray, then the people have nowhere to put hand or foot. Therefore the gentleman uses only such language as is proper for speech, and only speaks of what it would be proper to carry into effect. The gentleman in what he says leaves nothing to mere chance.” Inspired by these views, we make the analogy that the progress of science and the language used to describe it are two entangled electrons. This entanglement highlights the importance of introducing systemic names for enzymes using EC classification and the ever-growing problem of protein names (McDonald and Tipton, 2021). Here, we tackle one specific case of iron-sulfur ([FeS]) enzymes. We show that the language used to describe a conserved [FeS] enzyme of the innate immune system, i.e., viperin or RSAD2, is now inadequate and disentangled from its science. We discuss that the enzyme has cellular functions beyond its antiviral activity and that eukaryotic and prokaryotic enzymes catalyse the same chemical reactions. To prevent bias towards antiviral activity while studying various biochemical activities of the enzyme and using scientifically incorrect terms like “prokaryotic viperins,” we rectify the language describing the enzyme. Based on NC-IUBMB recommendations, we introduce the nomenclature S-adenosylmethionine (SAM) dependent Nucleotide Dehydratase (SAND).
| Item Type: | Article |
|---|---|
| Additional Information: | Funding information: European Cooperation in Science and Technology (COST) Action CA21115. |
| Uncontrolled Keywords: | antiviral,dehydratase,innate immun system,iron-sulfur [fes] cluster,nucleotide analogue,biochemistry,molecular biology,biochemistry, genetics and molecular biology (miscellaneous) ,/dk/atira/pure/subjectarea/asjc/1300/1303 |
| Faculty \ School: | Faculty of Science > School of Chemistry (former - to 2024) |
| UEA Research Groups: | Faculty of Science > Research Groups > Chemistry of Life Processes Faculty of Science > Research Centres > Centre for Molecular and Structural Biochemistry |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2022 12:30 |
| Last Modified: | 19 Oct 2024 00:00 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/89344 |
| DOI: | 10.3389/fmolb.2022.1032220 |
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