Scholarly record
COMPARATIVE GENOMICS OF THE SINORHIZOBIAL PHILM21-LIKE INTACT PROPHAGES ON COMPLETE CHROMOSOMES
Abstract
Soil saprophytic nitrogen-fixing nodule bacteria (rhizobia) of the Sinorhizobium meliloti species are formed symbiosis with alfalfa and can also be a host of bacteriophages. Rhizobia have a symbiotic and saprophytic life phase?s cycle. Nodules formed by rhizobia on alfalfa roots are destroyed at the end of the growing season and bacteria surviving in nodule threads and did not transformed into bacteroids are released into the soil microbiome. The last is enriched in bacteriophages, which can significantly decrease viability and population density of rhizobia. Bacteriophages can cause lytic infection, accompanied by reprogramming of the host metabolism, destruction of the host cell, or can integrate into the bacterial chromosome as prophages in the result of lysogenic infection that and transmitted to future generations. In this work, sequences of chromosomes of 22 S. meliloti strains deposited in GenBank with additional two strains the AK555 and CXM1-105 strains (sequenced in the framework of the RSF17-16-01095 project) were evaluated for prophages by PHASTER web server. ORFs and protein sequences were analyzed by BLASTn and BLASTp, respectively. Phylogenetic analysis was performed by IQTree (ML). The 18 sequences of intact phiLM21-like (phiLM21, NC_029046) prophages were detected in the chromosomes of the 14 different S. meliloti strains. The sizes of phiLM21-like prophages ranged from 50.8 to 69kb in length. The GC-content (%) of prophages varied from 59.2 to 60.8 and contained from 55 to 90 ORFs. Prophages were integrated into different tRNA genes located in the second and third quarters of the chromosome counting from the oriC. Revealed phiLM21-like prophages contained 3 types of integrases. The 11 out of 16 integrases were homologous on 26% to integrase from Azospirillum phage Cd (YP_001686913.1), the other 4 showed homology (37%) to integrase from Caulobacter phage Cr30 (YP_009098910.1) and the last one was on 81.6% identical to the integrase of the phiLM21 bacteriophage (YP_009221472.1). It was established that more than 50% of all ORFs encoded genes were homologous to phage genes, among which were ORFs encoding head and tail of the virion. Obtained data strongly evident that a high recombination activity is occurred between phages, as well as prophages are actively participated in horizontal gene transfer in a phage-bacteria-phage interaction frame. This work was financially supported by RSF 20-16-00105.
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