Data from: Evolutionary ecology of beta-lactam gene clusters in animals

Beta-lactam biosynthesis was thought to occur only in fungi and bacteria, but we recently reported the presence of isopenicillin N synthase in a soil-dwelling animal, Folsomia candida. However, it has remained unclear whether this gene is part of a larger beta-lactam biosynthesis pathway and how widespread the occurrence of penicillin biosynthesis is among animals. Here, we analyzed the distribution of beta-lactam biosynthesis genes throughout the animal kingdom and identified a beta-lactam gene cluster in the genome of F. candida (Collembola), consisting of isopenicillin N synthase (IPNS), δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS), and two cephamycin C genes (cmcI and cmcJ) on a genomic scaffold of 0.76 Mb. All genes are transcriptionally active and are inducible by stress (heat shock). A beta-lactam compound was detected in vivo using an ELISA beta-lactam assay. The gene cluster also contains an ABC transporter which is co-regulated with IPNS and ACVS after heat shock. Furthermore, we show that different combinations of beta-lactam biosynthesis genes are present in over 60% of springtail families but they are absent from genome- and transcript libraries of other animals including close relatives of springtails (Protura, Diplura, and insects). The presence of beta-lactam genes is strongly correlated with an eudaphic (soil-living) lifestyle. Beta-lactam genes IPNS and ACVS each form a phylogenetic clade in between bacteria and fungi, while cmcI and cmcJ genes cluster within bacteria. This suggests a single horizontal gene transfer event most probably from a bacterial host, followed by differential loss in more recently evolving species.长期以来，学界认为β-内酰胺（beta-lactam）类化合物的生物合成仅发生于真菌与细菌中，但我们近期在土壤栖息动物弹尾虫（Folsomia candida）中检测到了青霉素N合酶（isopenicillin N synthase, IPNS）的存在。然而，该基因是否属于更庞大的β-内酰胺生物合成通路，以及青霉素生物合成在动物界中的分布广度如何，仍未明确。本研究对β-内酰胺生物合成基因在整个动物界的分布情况进行了分析，并在弹尾虫（Folsomia candida，隶属弹尾纲（Collembola））的基因组中鉴定出一处β-内酰胺基因簇：该基因簇位于一段0.76 Mb的基因组支架上，包含青霉素N合酶（IPNS）、δ-(L-α-氨基己二酰)-L-半胱氨酰-D-缬氨酸合成酶（δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase, ACVS），以及两个头孢霉素C相关基因cmcI与cmcJ。所有基因均具有转录活性，且可在胁迫（热激）条件下被诱导表达。通过酶联免疫吸附测定（ELISA）的β-内酰胺检测方法，我们在弹尾虫体内检测到了β-内酰胺类化合物。该基因簇还包含一个ABC转运蛋白（ABC transporter），其在热激后与IPNS和ACVS协同调控表达。此外，我们发现超过60%的弹尾虫科类群中存在不同组合的β-内酰胺生物合成基因，但在其他动物（包括弹尾虫的近缘类群原尾虫纲（Protura）、双尾虫纲（Diplura）以及昆虫）的基因组与转录组文库中均未检出此类基因。β-内酰胺基因的存在与土壤栖息的生活方式显著相关。系统发育分析显示，IPNS与ACVS各自形成了一个介于细菌与真菌之间的演化支，而cmcI与cmcJ基因则聚类于细菌类群中。这表明该基因簇可能通过单次水平基因转移（horizontal gene transfer）事件从细菌宿主获得，随后在较晚演化出现的物种中发生了差异化的基因丢失。