Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication

Haruka Arashida,Haruka Odake,Ryota Noda,Shusei Sato,Satoshi Ohkubo,Hisayuki Mitsui,Masayuki Sugawara,Kiwamu Minamisawa,Kaori Kakizaki

doi:10.1038/s41396-021-01035-4

Abstract

Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA deletions that encompassed T3SS (rhc) and N2 fixation (nif) genes and were bounded by insertion sequence (IS) copies in direct orientation, indicating homologous recombination between ISs. Similar deletion events were observed in B. diazoefficiens USDA110 and B. japonicum J5. When we cultured a USDA122 strain with a marker gene sacB inserted into the rhc gene cluster, most sucrose-resistant mutants had deletions in nif/rhc gene clusters, similar to the mutants above. Some deletion mutants were unique to the sacB system and showed lower competitive nodulation capability, indicating that IS-mediated deletions occurred during free-living growth and the host plants selected the mutants. Among 63 natural bradyrhizobial isolates, 2 possessed long duplications (261–357 kb) harboring nif/rhc gene clusters between IS copies in direct orientation via homologous recombination. Therefore, the structures of symbiosis islands are in a state of flux via IS-mediated duplications and deletions during rhizobial saprophytic growth, and host plants select mutualistic variants from the resultant pools of rhizobial populations. Our results demonstrate that homologous recombination between direct IS copies provides a natural mechanism generating deletions and duplications on symbiosis islands.

Highlights

Symbiotic organisms can co-evolve through adaptive changes in the organization of the functional elements in their genomes
Bioinformatic prediction of insertion sequence (IS)-mediated deletions In a previous study, we determined that two ISs in direct orientation on symbiosis island A (SymA) of B. diazoefficiens USDA122 were involved in three types of deletions in the USDA122 genome [31]
When we subjected the USDA122 genome to a BlastN search with the IS elements as query sequences, A total of 63 copies of 15 different IS elements were found, 37 copies of which were located within SymA (Fig. 1A; Table S1)

Summary

Introduction

Symbiotic organisms can co-evolve through adaptive changes in the organization of the functional elements in their genomes. In animal–bacteria symbiosis, the evolution of obligate symbiont bacteria with intercellular lifestyles has been accompanied by a marked reduction in genome size [1,2,3]. The best-studied plant–bacteria symbiosis involves legume plants and nitrogen-fixing bacteria called rhizobia [3, 4]. Rhizobia have repeated symbiotic phases (in the plant) and free-living phases (in the soil) [4, 5]. Rhizobia generally possess the distinct packages of symbiosis genes (symbiosis islands or symbiotic plasmids) within their genome [3, 4, 6]. Bradyrhizobium species are thought to be ancestral rhizobia, because Bradyrhizobium, which shows enormous species diversity (>800 species), nodulates primitive leguminous plants [6, 8, 9]

Methods

Results

Conclusion