Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family
Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family
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DOI：
10.1073/pnas.1903161116
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发表时间：
2019-10-01
影响因子：
11.1
通讯作者：
Butler, Alison
中科院分区：
文献类型：
--
作者：
Reitz, Zachary L.;Hardy, Clifford D.;Butler, Alison
生物合成途径的基因组挖掘简化了次级代谢物的发现，但可能在预测结构中留下模糊性，这必须通过实验加以纠正。通过将生物合成基因簇预测的反应性与已验证的结构相结合，报道了铁载体中β -羟基天冬氨酸二对映体的来源。非血红素铁(II)/ α -酮戊二酸依赖的天冬氨酸β -羟化酶在铁载体生物合成基因簇中被鉴定出两种功能亚型，它们在基因组组织上不同——存在于非核糖体肽合成酶（NRPS）的羧基端作为融合结构域（I β H-Asp）或作为独立的酶（T β H-Asp）——每一种都对Asp β -羟化具有相反的立体选择性。在pyoverdine GB-1、delftibactin、histiorrugatin和cupriachhelin中β - ohasp残基的立体化学表征证实了这种亚型描述的预测能力。alterobactin的l - thro (2S, 3S) β - ohasp残基是由整合到NRPS AltH的β -羟化酶结构域羟基化产生的，而delftibactin中的L-erythro (2S, 3R) β - ohasp是由独立的β -羟化酶DelD产生的。cupriachhelin含有L-三o和L-红细胞β - ohasp，与生物合成基因簇中存在两种类型的β -羟化酶一致。第三种亚型的非血红素铁(II)/ α -酮戊二酸依赖酶（I β HHis）羟基化组氨酸残基具有l -三羧基立体特异性。先前描述的NRPS缩合结构域超家族的非规范成员被确定，称为界面结构域，它被提议在羟基化之前定位β -羟化酶和NRPS结合的氨基酸。通过将表征的β - ohasp非对映体映射到铁载体β -羟化酶的系统发育树上，实现了β - ohasp硅立体化学预测的方法。
Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the beta-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/alpha-ketoglutarate-dependent aspartyl beta-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization-existing either as fused domains (I beta H-Asp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (T beta H-Asp)-and each directs opposite stereoselectivity of Asp beta-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of beta-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The L-threo (2S, 3S) beta-OHAsp residues of alterobactin arise from hydroxylation by the beta-hydroxylase domain integrated into NRPS AltH, while L-erythro (2S, 3R) beta-OHAsp in delftibactin arises from the stand-alone beta-hydroxylase DelD. Cupriachelin contains both L-threo and L- erythro beta-OHAsp, consistent with the presence of both types of beta-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/alpha-ketoglutarate-dependent enzymes (I beta HHis) hydroxylates histidyl residues with L-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the beta-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized beta-OHAsp diastereomers to the phylogenetic tree of siderophore beta-hydroxylases, methods to predict beta-OHAsp stereochemistry in silico are realized.