A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin.
Peptide antibiotics are typically biosynthesized by one of two distinct machineries in a ribosome-dependent or ribosome-independent manner. Pheganomycin (PGM (1)) and related analogs consist of the nonproteinogenic amino acid (S)-2-(3,5-dihydroxy-4-hydroxymethyl)phenyl-2-guanidinoacetic acid (2) and a proteinogenic core peptide, making their origin uncertain. We report the identification of the biosynthetic gene cluster from Streptomyces cirratus responsible for PGM production. Unexpectedly, the cluster contains a gene encoding multiple precursor peptides along with several genes plausibly encoding enzymes for the synthesis of amino acid 2. We identified PGM1, which has an ATP-grasp domain, as potentially capable of linking the precursor peptides with 2, and validate this hypothesis using deletion mutants and in vitro reconstitution. We document PGM1's substrate permissivity, which could be rationalized by a large binding pocket as confirmed via structural and mutagenesis experiments. This is to our knowledge the first example of cooperative peptide synthesis achieved by ribosomes and peptide ligases using a peptide nucleophile.
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Motoyoshi
M
Noike
Institute of Natural Medicine, University of Toyama, Toyama, Japan.
Takashi
T
Matsui
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Koichi
K
Ooya
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Ikuo
I
Sasaki
Institute of Natural Medicine, University of Toyama, Toyama, Japan.
Shouta
S
Ohtaki
Department of Bioscience, Fukui Prefectural University, Fukui, Japan.
Yoshimitsu
Y
Hamano
Department of Bioscience, Fukui Prefectural University, Fukui, Japan.
Chitose
C
Maruyama
National Institute of Infectious Diseases, Tokyo, Japan.
Jun
J
Ishikawa
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Yasuharu
Y
Satoh
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Hajime
H
Ito
Institute of Natural Medicine, University of Toyama, Toyama, Japan.
Hiroyuki
H
Morita
Graduate School of Engineering, Hokkaido University, Hokkaido, Japan.
Tohru
T
Dairi
D000900:Anti-Bacterial Agents / Q000096:biosynthesis*; D008025:Ligases / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D016296:Mutagenesis; D010455:Peptides / Q000378:metabolism*; D011487:Protein Conformation; D012270:Ribosomes / Q000378:metabolism*; D013302:Streptomyces / Q000235:genetics / Q000378:metabolism
D000900:Anti-Bacterial Agents; D010455:Peptides; C000595498:pheganomycin; D008025:Ligases