Related Experiment Video
Updated: Jun 10, 2025
Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)
Published on: March 16, 2012
Hot Spots of Site-Specific Integration into the Sinorhizobium meliloti Chromosome
Maria E Vladimirova1, Marina L Roumiantseva1, Alla S Saksaganskaia1
1Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia.
Abstract:
The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as Sinorhizobium meliloti, were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to 88.98 kb, were identified in the genomes of 27 S. meliloti strains. The amount of genetic information foreign to S. meliloti accumulated in all identified PRSs was 6.30 Mb. However, more than 53% of this information was contained in prophages (Phs) and genomic islands (GIs) integrated into genes encoding tRNAs (tRNA genes) located on the chromosomes of the rhizobial strains studied. It was found that phiLM21-like Phs were predominantly abundant in the genomes of S. meliloti strains of distant geographical origin, whereas RR1-A- and 16-3-like Phs were much less common. In addition, GIs predominantly contained fragments of phages infecting bacteria of distant taxa, while rhizobiophage-like sequences were unique. A site-specific integration analysis revealed that not all tRNA genes in S. meliloti are integration sites, but among those in which integration occurred, there were "hot spots" of integration into which either Phs or GIs were predominantly inserted. For the first time, it is shown that at these integration "hot spots", not only is the homology of attP and attB strictly preserved, but integrases in PRSs similar to those of phages infecting the Proteobacteria genera Azospirillum or Pseudomonas are also present. The data presented greatly expand the understanding of the fate of phage-related sequences in host bacterial genomes and also raise new questions about the role of phages in bacterial-phage coevolution.
Insights
This study identified 314 phage-related sequences (PRSs) in Sinorhizobium meliloti, with over half integrated into tRNA genes. Specific integration "hot spots" and phage integrases were observed, advancing our understanding of bacterial-phage coevolution.
Area of Science:
- Microbiology
- Genomics
- Bacteriology
Background:
- Nitrogen-fixing root nodule bacteria like Sinorhizobium meliloti are agriculturally important.
- Phage-related sequences (PRSs) and their integration into bacterial genomes are key factors in bacterial evolution and phage-host interactions.
- Understanding the diversity and integration patterns of PRSs in S. meliloti provides insights into genome plasticity and bacterial adaptation.
Purpose of the Study:
- To investigate the diversity and genomic integration of phage-related sequences (PRSs) in Sinorhizobium meliloti.
- To identify specific integration sites and characterize the genetic elements involved in PRS integration.
- To explore the evolutionary implications of PRS integration in agriculturally valuable bacteria.
Main Methods:
- Bioinformatic analysis of 27 S. meliloti genomes to identify and characterize 314 PRSs.
- Analysis of PRS size, foreign genetic information content, and integration sites, particularly tRNA genes.
- Comparative analysis of PRS types (prophages, genomic islands) and their geographical distribution.
- Investigation of integrase genes and attP/attB homology at integration hot spots.
Main Results:
- 314 PRSs (3.24–88.98 kb) were identified, contributing 6.30 Mb of foreign DNA in S. meliloti.
- Over 53% of foreign DNA was found in prophages (Phs) and genomic islands (GIs) integrated into tRNA genes.
- phiLM21-like Phs were abundant in geographically distant strains; GIs contained fragments of distantly related phages.
- Specific tRNA 'hot spots' were identified for Ph and GI integration, preserving attP/attB homology and featuring phage integrases.
Conclusions:
- The study reveals extensive PRS diversity and integration into S. meliloti genomes, primarily within tRNA genes.
- Identified integration 'hot spots' and associated integrases highlight specific mechanisms governing PRS integration.
- These findings significantly enhance the understanding of phage-host dynamics and bacterial genome evolution.
More Related Videos
20:01Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti
Published on: October 1, 2013
09:38Site-Directed φC31-Mediated Integration and Cassette Exchange in Anopheles Vectors of Malaria
Published on: February 2, 2021
