Evolution of Insertion Sequences in Rhizobium

Insertion sequences (ISs) are mobile elements constituted basically by a gene that encodes the transposase (an enzyme required for transposition) and invert repeat sequences (IRs) at both sides. ISs have been grouped in different families according to their similarity, transposase type, transposition mechanism and the sequence of the IRs. The representation of the ISs families varies widely among bacteria. Some species lack of the ISs, whereas others contain more than 100 ISs of different families or belong to only one predominant family. Neither the origin of ISs nor their cellular function is known, except for some of them that code for adaptive phenotypes (e. g. antibiotic resistance).

There are numerous ISs in the genomes of the symbiotic nitrogen fixing bacteria already sequenced. Particularly, they are abundant in symbiotic plasmids and symbiotic islands. In R. etli CFN42 there are 153 ORFs related to ISs. They are distributed in the symbiotic plasmid p42d, the conjugative plasmid p42a, and in the chromosome. There are no ISs in the other four plasmids (p42b, p42c, p42e, p42f) that compose the genome of the R. etli CFN42 strain. It is also noteworthy that no ISs interrupt any ORF, known or hypothetical. Altogether, these observations indicate that ISs are associated to horizontal gene transfer through conjugative plasmids. Therefore, they might represent a link with the origin of symbiosis and the life-style of R. etli. The project aims to answer the following questions:

  1. What is the distribution of IS families among the species of the order Rhizobiales?
  2. What is the degree of divergence among the ISs of the same family across species of the order Rhizobiales?
  3. Do the ISs are subjected to selective pressures?
  4. What is the dynamic of ISs in the R. etli population?
  5. Do they are inherited by vertical or horizontal descendence?

Currently we have started a systematic search for ISs into the complete genomes available for species of the order Rhizobiales. It should produce a map of the distribution and preponderance of the ISs, as well as a first sight of their dynamics. Taken the already characterized ISs of the genome of R. etli, we are looking for the homologous ISs into syntenic regions of R. etli strains of distinct geographical locations and from a single locality. Inferences about ISs movement will be drawn from the differences in the size of the amplified fragments for homologous regions of the genome. Finally, phylogenetic analysis will be employed to reconstruct the dynamic of one or two IS families across the species of the order Rhizobiales.

Participants .

M. C. Luis Lozano, design, performs experiments, and data analysis.
Dr. Víctor González, design experiments, and data analysis.
Dr. Guillermo Dávila, data analysis.

Evolutionary Genomics Program