Characterization of a C3 Deoxygenation Pathway Reveals a Key Branch Point in Aminoglycoside Biosynthesis.
Apramycin is a clinically interesting aminoglycoside antibiotic (AGA) containing a highly unique bicyclic octose moiety, and this octose is deoxygenated at the C3 position. Although the biosynthetic pathways for most 2-deoxystreptamine-containing AGAs have been well characterized, the pathway for apramycin biosynthesis, including the C3 deoxygenation process, has long remained unknown. Here we report detailed investigation of apramycin biosynthesis by a series of genetic, biochemical and bioinformatical studies. We show that AprD4 is a novel radical S-adenosyl-l-methionine (SAM) enzyme, which uses a noncanonical CX3CX3C motif for binding of a [4Fe-4S] cluster and catalyzes the dehydration of paromamine, a pseudodisaccharide intermediate in apramycin biosynthesis. We also show that AprD3 is an NADPH-dependent reductase that catalyzes the reduction of the dehydrated product from AprD4-catalyzed reaction to generate lividamine, a C3' deoxygenated product of paromamine. AprD4 and AprD3 do not form a tight catalytic complex, as shown by protein complex immunoprecipitation and other assays. The AprD4/AprD3 enzyme system acts on different pseudodisaccharide substrates but does not catalyze the deoxygenation of oxyapramycin, an apramycin analogue containing a C3 hydroxyl group on the octose moiety, suggesting that oxyapramycin and apramycin are partitioned into two parallel pathways at an early biosynthetic stage. Functional dissection of the C6 dehydrogenase AprQ shows the crosstalk between different AGA biosynthetic gene clusters from the apramycin producer Streptomyces tenebrarius, and reveals the remarkable catalytic versatility of AprQ. Our study highlights the intriguing chemistry in apramycin biosynthesis and nature's ingenuity in combinatorial biosynthesis of natural products.
Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.
Meinan
M
Lv
Department of Chemistry, Fudan University , Shanghai, 200433, China.
Xinjian
X
Ji
Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.|Department of Chemistry, Fudan University , Shanghai, 200433, China.
Junfeng
J
Zhao
Department of Chemistry, Fudan University , Shanghai, 200433, China.
Yongzhen
Y
Li
Department of Chemistry, Fudan University , Shanghai, 200433, China.
Chen
C
Zhang
Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.
Li
L
Su
Department of Chemistry, Fudan University , Shanghai, 200433, China.
Wei
W
Ding
Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.
Zixin
Z
Deng
Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.
Yi
Y
Yu
Department of Chemistry, Fudan University , Shanghai, 200433, China.
Qi
Q
Zhang
D000617:Aminoglycosides / Q000378:metabolism; D002240:Carbohydrate Sequence; D002384:Catalysis; D009328:Nebramycin / Q000031:analogs & derivatives* / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism; D010088:Oxidoreductases / Q000378:metabolism; D010100:Oxygen / Q000737:chemistry*; D013379:Substrate Specificity
D000617:Aminoglycosides; D009328:Nebramycin; C011666:apramycin; C005936:paromamine; D010088:Oxidoreductases; D010100:Oxygen