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Plant Nodulation Inducers Enhance Horizontal Gene Transfer of Azorhizobium Caulinodans Symbiosis Island

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Plant Nodulation Inducers Enhance Horizontal Gene Transfer of Azorhizobium Caulinodans Symbiosis Island Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island Jun Linga,1, Hui Wanga,1, Ping Wua, Tao Lia, Yu Tanga, Nawar Naseerb, Huiming Zhenga, Catherine Masson-Boivinc, Zengtao Zhonga,c,2, and Jun Zhua,b,2 aDepartment of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; bDepartment of Microbiology, University of Pennsylvania, Philadelphia, PA 19104; and cInstitut National de la Recherche Agronomique, UMR 441, Laboratoire des Interactions Plantes-Microorganismes, Castanet-Tolosan 31326, France Edited by Bonnie L. Bassler, Princeton University and Howard Hughes Medical Institute, Princeton, NJ, and approved October 19, 2016 (received for review September 9, 2016) Horizontal gene transfer (HGT) of genomic islands is a driving force of program leading to nodule organogenesis (7). Nod factors are bacterial evolution. Many pathogens and symbionts use this mech- lipochito-oligosaccharides of diverse structures and the major anism to spread mobile genetic elements that carry genes important determinants of host specificity. Rhizobia have evolved via hor- for interaction with their eukaryotic hosts. However, the role of the izontal transfer of essential nodulation and nitrogen fixation host in this process remains unclear. Here, we show that plant genes that are carried by either large plasmids or genomic is- compounds inducing the nodulation process in the rhizobium-legume lands. Exchange of symbiotic material between rhizobial species mutualistic symbiosis also enhance the transfer of symbiosis islands. and genera has been frequent during evolution (8). The symbiosis We demonstrate that the symbiosis island of the Sesbania rostrata islands of the Mesorhizobium, Azorhizobium,andBradyhizobium symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and species are mainly located on the chromosome (9–11). For conjugative element (ICEAc) that is able to excise, form a circular example, the rhizobium strain Mesorhizobium loti R7A has a DNA, and conjugatively transfer to a specific site of gly-tRNA gene 502-kb ICE called ICEMlSymR7A that contains genes required of other rhizobial genera, expanding their host range. The HGT for nitrogen-fixing symbiosis with Lotus corniculatus (12). The frequency was significantly increased in the rhizosphere. An ICEAc- ICEMlSymR7A is inserted downstream of a phe-tRNA gene in located LysR-family transcriptional regulatory protein AhaR trig- the M. loti chromosome and can be transferred to nonsymbiotic MICROBIOLOGY gered the HGT process in response to plant flavonoids that induce mesorhizobia both in the laboratory and in the field, converting the expression of nodulation genes through another LysR-type pro- these strains into symbionts of L. corniculatus (12, 13). The tein, NodD. Our study suggests that rhizobia may sense rhizosphere transfer of ICEMlSymR7A is mediated by quorum sensing and is environments and transfer their symbiosis gene contents to other controlled by a complex multipartite regulatory system involving genera of rhizobia, thereby broadening rhizobial host-range an excisionase and an excision activator produced via a pro- specificity. grammed ribosomal frameshift (14–16). Here, we provide evidence that, in the S. rostrata-Azorhizobium horizontal gene transfer | host-range | integrative and caulinodans system, the symbiotic process and the symbiosis island conjugative element | naringenin | nodulation transfer are triggered by the same plant compound. The symbiosis island of A. caulinodans is an 87.6-kb integrative and conjugative Ac orizontal gene transfer (HGT) plays a major role in the element (ICE ) that is able to excise, form a circular DNA, and Hbiodiversity and ecology of bacteria by contributing to their conjugatively transfer to a specific site of gly-tRNA gene of various adaptability, fitness, and competitiveness (1). Gene acquisition rhizobial species, allowing them to stem nodulate S. rostrata. The Ac Ac involves mobile genetic elements (MGEs), such as plasmids and ICE transfer is enhanced by an ICE -located LysR-family genomic islands. Large MGEs can provide complex novel traits, protein, AhaR, in response to the plant flavonoid compounds such as virulence and mutualistic traits that enable bacteria to interact with eukaryotic hosts (2). However, the role of the host Significance in the transfer of MGE is poorly documented. One type of MGE that is widespread in prokaryotic genomes is called integrative Pathogenic or symbiosis islands are mobile genetic elements and conjugative elements (ICEs) (3). ICEs are self-transmissible that can provide recipient bacteria the capacity to establish mobile elements that carry genes encoding the machinery for intimate interactions with eukaryotic hosts. For example, le- DNA processing and transferring. These genes allow ICEs to gume symbionts have evolved via horizontal transfer of sym- excise themselves from the chromosome and form a closed cir- biotic plasmids or genomic islands. Here, we show that the cular molecule, conjugate, and site-specifically recombine into transfer of the symbiosis island of the Sesbania rostrata sym- recipient chromosomes. ICEs have been found to render a di- biont, Azorhizobium caulinodans, to other rhizobia is enhanced verse range of characteristics on the bacteria that carry them, by plant flavonoids that also serve as signals to initiate the including resistance to antibiotics and heavy metals, the ability to symbiotic process. These data suggest that eukaryotic hosts are degrade aromatic compounds, and promotion of biofilm for- involved in bacterial horizontal gene transfer to promote symbi- mation. Some ICEs carry traits such as virulence and symbiosis. otic interactions between rhizobia and legumes. Rhizobia are facultative endosymbionts that are able to form Author contributions: J.L., H.W., P.W., C.M.-B., Z.Z., and J.Z. designed research; J.L., H.W., nitrogen-fixing nodules on the root of legume hosts (4). Some P.W., T.L., Y.T., N.N., and H.Z. performed research; J.L., H.W., Z.Z., and J.Z. analyzed data; tropical legumes, such as Sesbania rostrata, are also nodulated on and J.L., H.W., N.N., C.M.-B., and J.Z. wrote the paper. the stem by their rhizobial partners (5). Initiation of symbiosis The authors declare no conflict of interest. requires a two-way signal exchange program involving plant This article is a PNAS Direct Submission. compounds and bacterial nodulation (nod) genes (6). The con- 1J.L. and H.W. contributed equally to this work. served LysR-family transcriptional regulator NodD perceives 2To whom correspondence may be addressed. Email: [email protected] or flavonoid signals released by the host legume, and activates nod [email protected]. genes that encode enzymes responsible for the synthesis of sig- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. naling Nod factors, which trigger the plant developmental 1073/pnas.1615121113/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1615121113 PNAS Early Edition | 1of6 Downloaded by guest on September 25, 2021 that also induce the expression of the A. caulinodans nodulation were present. To study the excision and integration of ICEAc, the genes, implying that rhizobia may sense rhizosphere environments hallmark characteristics of diverse integrative and conjugative and modulate their genetic programs to induce both symbiotic and elements (3), we designed a set of primers that are specific for HGT machineries. sequences of either the donor or the recipients (Fig. 1 A and B and SI Appendix, Table S2). Using primer pairs m1-a2 and m4- Results a3, PCR products were detected in M. huakuii harboring ICEAc A. caulinodans Symbiosis Island ICEAc Can Horizontally Transfer to (Mh::ICEAc), but not in wildtype M. huakuii (Mh) (Fig. 1B), in- Other Rhizobial Genera. Analysis of the A. caulinodans ORS571 dicating the integration of ICEAc into the M. huakuii genome. genome (10) revealed that its 87.6-kb symbiosis region, which We also detected an ICE circular form in both A. caulinodans contains three nodulation loci that are involved in the bio- and Mh::ICEAc by using the primer pair a2-a3 (Fig. 1B), in- synthesis of Nod factors, has typical characteristics of a symbiosis dicative of excision events. The effect of growth phase on the island: It has a lower GC content and is inserted adjacent to a gly- excision of ICEAc was investigated by quantitative PCR (qPCR) tRNA gene. This region also contains genes related to conjugal of DNA purified from A. caulinodans cultures at different growth transfer, transposases, and integrases (Fig. 1A and SI Appendix, stages. Fig. 1C shows that excision products were present at low Fig. S1), suggesting that it may facilitate horizontal gene transfer frequency in log-phase growth cells but increased in the stationary events. To examine whether this symbiosis island (ICEAc) is able phase. Collectively, these data suggest that the A. caulinodans to transfer to other rhizobia, we inserted a kanamycin-resistant symbiosis island is an integrative and conjugative element that can cassette (KmR) into an intergenic region of ICEAc in wild-type excise from the chromosome to form a circular intermediate and A. caulinodans ORS571 (Fig. 1A). We then mixed the resulting conjugally transfer to different genera of rhizobia. strain with other rhizobial species and examined whether re- cipient strains acquired kanamycin resistance. We found that Conjugation Apparatus and an Integrase Are
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