Complex evolution of integrases of Bradyrhizobium symbiosis islands

One of the remarkable discoveries from bacterial genomics are genomic islands. In the nitrogen fixing bacteria that form nodules in legumes, namely in Bradyrhizobium and Mesorhizobium there are symbiosis islands that contain genes for nodulation, nitrogen fixation, host specificity and also the integrases that are required to transfer of genomic islands. However only in some cases, symbiosis islands may be transferred among related bacteria. Symbiosis islands are distinguished by their low CG content. The protein structure analysis of an integrase from the symbiosis island of a Bradyrhizobium strain obtained from the legume tree Inga vera was inferred with Alphafold showing its binding to DNA. Here we present a phylogenetic study of bradyrhizobial integrases. Our analysis indicated that bradyrhizobial integrases are basal to those from gammaporteobacteria suggesting that they emerged earlier. A single integrase gene was found both in alpha and gammaproteobacterial and we found that it corresponded to a phage integrase. We detected in some cases phylogenetic similarities of integrases even among unrelated non-nodulating bacteria suggesting horizontal gene transfer. In other cases, the integrase genes are pseudogenes that would not drive mobility. In addition, integrases may not follow plant specificity. Symbiosis islands may constitute megaintegrons or superintegrons being collectors of genes including integrases.