Biosynthetic Gene Cluster of Linaridin Peptides Contains Epimerase Gene


Amino acids are the building blocks of enzymes, receptors, antibodies, signaling molecules, hormones, and several other crucial protein structures found in all living things. The body can get its D-amino acids from a variety of places. First off, endogenous biosynthesis of D-amino acids results from the racemization of L-amino acids by racemase enzymes. Serine racemase and aspartate racemase are the only racemase enzymes currently known to exist in mammals. Only serine racemase has been identified in human tissue out of these two enzymes. The ever-expanding genome studies of the past two decades have uncovered a significant class of natural compounds called ribosomally produced and post-translationally modified peptides (RiPPs). These peptide-based natural products are made from ribosomally produced precursor peptides, which typically have a C-terminal core peptide where post-translational modifications take place and an N-terminal leader peptide that binds to the RiPP recognition element (RRE) of the modifying enzymes. A developing family of RiPPs known as linaridins has the name-bearing linear peptidyl structure with many dehydrated (arid) amino acids. The RiPP family is widely distributed in nature, despite the fact that only a small number of linaridins have been structurally described to yet. The ability to divide these substances into three subfamilies is made possible by the highly conserved leader regions and various cores of linaridin precursor peptides. Salinipeptins, which include 22 amino acid residues and several D-amino acids, are part of the type-A linaridin class of post-translationally modified peptides (RiPPs). The biosynthetic gene clusters of type-A linaridins share identical gene organisation, despite the fact that chirality of other type-A linaridins, including grisemycin and cypemycin, has not been observed.

In a new paper published in ChemBioChem research journal, Hokkaido University investigators Wanlu Xiao, Assitant Professor Yasuharu Satoh, Associate Professor Yasushi Ogasawara and Professor Tohru Dairi revealed heterologous expression of grisemycin biosynthetic gene cluster (grm) and demonstrated that grisemycin contains several D-amino acids, comparable to salinipeptins. They used type-A linaridin clusters to verify their theory and checked to see if the metabolites included D-amino acid residues.

The research team originally looked at the grisemycin cluster because they were unable to get producer strains of salinipeptin and cypemycin. To express grm cluster in Streptomyces lividans, a heterologous host which does not produce grisemycin, the grm cluster from Streptomyces griseus was cloned into pWHM3, covering an area of around 7 kbp from grmA to grmP. The presence of D-amino acid residues was next tested as a common characteristic of type-A linaridins using heterologous production of two more gene clusters found in a publically accessible genome database. Three type-A linaridin biosynthetic gene clusters were heterologously expressed. All of the metabolites resembled salinipeptin A in that they all included numerous D-amino acids. These findings were significant since they strongly suggested that type-A linaridin clusters included the gene for a new peptide epimerase. Following that, researchers used gene deletion studies of the grm cluster to examine each gene’s function and showed that epimerization came before decarboxylation and methylation. Since the grmL gene is the only one in the cluster with an unknown function, GrmL may be responsible for the epimerization during the initial stages of biosynthesis. Since peptide site-specific epimerization is chemically difficult, several methods to enzymatically add D-amino acid residues to peptides have long been sought for.

In conclusion, the findings of Hokkaido University scientists unequivocally demonstrate the contribution of a new peptide epimerase in linaridin production. This research paves the way for future biochemical studies of the production of natural compounds in the linaridin family.

Biosynthetic Gene Cluster of Linaridin Peptides Contains Epimerase Gene - Medicine Innovates

About the author

Yasushi Ogasawara received his B.S. (2000) and Ph.D. (2005) degrees from the Tokyo Institute of Technology (Japan) under the supervision of Prof. Katsumi Kakinuma and Prof. Tadashi Eguchi. He studied with Prof. Hung-wen Liu at the University of Texas, Austin as a postdoctoral fellow (2005–2011) and then worked at the University of New Mexico (2012–2014) as a research assistant professor. He was appointed Assistant Professor at the Graduate School of Engineering, Hokkaido University in 2014 and he was promoted to Associate Professor in 2021. His current research focuses on natural product chemistry including (i) biosynthesis, (ii) in vitro and in vivo characterization of enzymes, and (iii) discovery of novel natural products.

About the author

Tohru Dairi received his B.Sc. (1983) and M.Sc. (1985) degrees from Nagoya University. From 1985 to 1994, he was at Kyowa Hakko Kogyo, Co. Ltd. After receiving his Ph.D. from the University of Tokyo (1982), he joined Toyama Prefectural University and studied genes and enzymes essential for the biosynthesis of natural products, especially isoprenoids produced by actinomycetes. Since 2010 he has been a professor at Hokkaido University. His research interests are novel microbial primary pathways, unique secondary metabolic pathways, and enzymes involved in these pathways.


Xiao W, Satoh Y, Ogasawara Y, Dairi T. Biosynthetic Gene Cluster of Linaridin Peptides Contains Epimerase Gene. ChemBioChem. 2022 May 12:e202100705.

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