Discovery of recombinases enables genome mining PNAS PLUS of cryptic biosynthetic gene clusters in Burkholderiales species Xue Wanga,1, Haibo Zhoua,1, Hanna Chena,b,1, Xiaoshu Jinga, Wentao Zhenga, Ruijuan Lia, Tao Suna, Jiaqi Liua, Jun Fua, Liujie Huoa, Yue-zhong Lia, Yuemao Shena, Xiaoming Dingc, Rolf Müllerd, Xiaoying Biana,2, and Youming Zhanga,2 aShandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, 266237 Qingdao, China; bHunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, People’s Republic of China; cCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 200433 Shanghai, China; and dDepartment of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 28, 2018 (received for review December 1, 2017) Bacterial genomes encode numerous cryptic biosynthetic gene RecE/RecT from Rac prophage, encoded in the E. coli chromosome clusters (BGCs) that represent a largely untapped source of drugs (10–13). Full-length RecE and RecT mediate linear−linear ho- or pesticides. Mining of the cryptic products is limited by the mologous recombination (LLHR), which can be used to directly unavailability of streamlined genetic tools in native producers. clone large DNA regions from genomic DNA into E. coli ex- Precise genome engineering using bacteriophage recombinases is pression vectors (14), while Redα and Redβ promote homolo- particularly useful for genome mining. However, recombinases gous recombination between linear and circular DNA molecule are usually host-specific. The genome-guided discovery of novel [linear plus circular homologous recombination (LCHR)]. In recombinases and their transient expression could boost cryptic addition, Redαβ recombineering is particularly relevant to bacterial BGC mining. Herein, we reported a genetic system employing Red genome engineering for genome mining, because the linear targeting recombinases from Burkholderiales strain DSM 7029 for efficient DNA carrying short homology regions (conveniently generated by genome engineering in several Burkholderiales species that currently PCR) is sufficient for gene modification, and dedicated targeting lack effective genetic tools. Using specialized recombinases-assisted plasmids are not required, unlike in single- or double-crossover in situ insertion of functional promoters, we successfully mined five mutagenesis (15). The Redαβ system from E. coli has been directly cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, applied to several closely related Gram-negative bacteria for genome two of which were silent. Two classes of lipopeptides, glidopeptins engineering, e.g., Salmonella enterica (16), Klebsiella pneumo- and rhizomides, were identified through extensive spectroscopic niae (17), Agrobacterium tumefaciens (18), Pantoea ananatis characterization. This recombinase expression strategy offers utility (19), and naturally transformable Burkholderia species (20, 21). within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities. Significance recombinases | genome mining | Burkholderiales | lipopeptide | natural product Natural products biosynthesized by cryptic gene clusters rep- resent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted acteria represent an important source of medicines and by the lack of streamlined genetic tools, especially in nonmodel pesticides (1, 2). Current genome sequencing projects have B biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe revealed a large number of biosynthetic gene clusters (BGCs), the discovery of a pair of bacteriophage recombinases and but their natural products have not yet been identified (3–5). The application of recombinase-assisted promoter engineering to enzymes encoded by these unexploited biosynthetic genes may rapidly identify and activate several cryptic biosynthetic gene synthesize metabolites that could serve as a reservoir of novel clusters in two Burkholderiales strains that currently lack ef- scaffolds for drug screening (6). Two major genome mining fective genetic tools. Construction of an efficient genome en- strategies, featuring homologous and heterologous expression, gineering platform in a natural product producer expedites were employed to mine cryptic BGCs (7). Homologous expres- mining of cryptic BGCs in their native backgrounds, and host sion in the native producers ensures proper substrates, precur- melioration for yield or structure optimization. This strategy MICROBIOLOGY sors, cofactors, and accessory factors for biosynthesis, which enables potentially scalable discovery of novel metabolites could maximize generation of cryptic BGC biosynthesis prod- with intriguing bioactivities from many other bacteria. ucts. However, this strategy requires efficient genetic manipu- lation tools in the producers to meet the demand of high- Author contributions: X.B. and Y.Z. designed research; X.W., H.Z., H.C., X.J., W.Z., T.S., and throughput genome mining in the postgenomic era. Recently, J.L. performed research; R.L. and J.F. contributed new reagents/analytic tools; X.W., H.Z., H.C., L.H., Y.-z.L., Y.S., X.D., R.M., X.B., and Y.Z. analyzed data; and X.W., H.Z., H.C., X.B., yeast homologous recombination and CRISPR-Cas9 strategies and Y.Z. wrote the paper. were harnessed to activate silent BGCs by promoter engineering The authors declare no conflict of interest. CHEMISTRY in metagenomic DNA and natural product proficient strepto- This article is a PNAS Direct Submission. mycetes, respectively (8, 9). However, in other natural product This open access article is distributed under Creative Commons Attribution-NonCommercial- producers, such as bacilli, Burkholderiales, myxobacteria, and NoDerivatives License 4.0 (CC BY-NC-ND). cyanobacteria, scalable and efficient genome manipulation is still 1X.W., H.Z., and H.C. contributed equally to this work. a frustrating challenge. 2To whom correspondence may be addressed. Email: [email protected] or Red/ET recombineering is an in vivo homologous recombination- [email protected]. based genetic engineering method employed primarily in Escherichia This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. coli by using short homology arms (∼50 bp) based on the expression of 1073/pnas.1720941115/-/DCSupplemental. either Redα/Redβ from the Red operon of λ phage or the analogous Published online April 16, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1720941115 PNAS | vol. 115 | no. 18 | E4255–E4263 Downloaded by guest on October 2, 2021 However, it is not functional in other Burkholderiales strains (20, recombinases were also applied to other Burkholderiales strains 21). In more distant species, host-specific Redαβ or RecET ho- that currently lack effective genetic tools and native Redαβ homo- molog systems are mandatory (22–29). logs, which resulted in the successful identification of two cryptic The order Burkholderiales belongs to β-Proteobacteria and NRPS BGCs. Two of five identified BGCs were silent (i.e., products includes several pathogenic bacteria and several environmental not detectable by liquid chromatography-mass spectrometry (LC- species. A number of Burkholderiales genomes contain plentiful MS) analysis in their native hosts under the given conditions). In putative natural product BGCs (4, 5, 30, 31). The proportion of addition, two classes of lipopeptides, glidopeptins and rhizomides, polyketide synthases (PKSs) and nonribosomal peptide synthe- were identified from DSM 7029 and Paraburkholderia rhizoxinica tases (NRPSs) in Burkholderia genomes is second only to that of HKI 454 (36), respectively. actinobacteria and is higher than that of bacilli, cyanobacteria, and myxobacteria (32). Burkholderia species also exhibit great Results biosynthetic potential for production of siderophores and lip- Host-Specific Phage-Derived Recombinase Pairs in Burkholderiales. It opeptides (31). Thus, Burkholderiales species have emerged as a had been shown that the Redαβ or RecET recombinases from new source of natural products with a plethora of BGCs still E. coli could not be applied to nonnaturally transformable Bur- cryptic or silent (31–34). To access these BGCs, it is urgent to kholderia strains (21). This study also confirmed that Redαβ was invent Burkholderiales specific homologous expression systems, not functional in the Burkholderiales strain DSM 7029 (Fig. 2). particularly, novel Red/ET recombinases from Burkholderiales BlastP analysis using the amino acid sequences from E. coli Redαβ strains for efficient genome engineering. or RecET as queries revealed 7 Redαβ-like and 10 RecET-like This study invented a workflow for the discovery of novel recombinase pairs in ∼1,000 Burkholderiales strains (most of which recombinases and the associated transient expression system to belong to Burkholderia and Paraburkholderia genera) (SI Appendix, facilitate in situ promoter insertion for cryptic BGC mining (Fig.