Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid.
Linear chromosomes are atypical in bacteria and likely a secondary trait derived from ancestral circular molecules. Within the Rhizobiaceae family, whose genome contains at least two chromosomes, a particularity of Agrobacterium fabrum (formerly A. tumefaciens) secondary chromosome (chromid) is to be linear and hairpin-ended thanks to the TelA protelomerase. Linear topology and telA distributions within this bacterial family was screened by pulse field gel electrophoresis and PCR. In A. rubi, A. larrymoorei, Rhizobium skierniewicense, A. viscosum, Agrobacterium sp. NCPPB 1650, and every genomospecies of the biovar 1/A. tumefaciens species complex (including R. pusense, A. radiobacter, A. fabrum, R. nepotum plus seven other unnamed genomospecies), linear chromid topologies were retrieved concomitantly with telA presence, whereas the remote species A. vitis, Allorhizobium undicola, Rhizobium rhizogenes and Ensifer meliloti harbored a circular chromid as well as no telA gene. Moreover, the telA phylogeny is congruent with that of recA used as a marker gene of the Agrobacterium phylogeny. Collectively, these findings strongly suggest that single acquisition of telA by an ancestor was the founding event of a large and diverse clade characterized by the presence of a linear chromid. This clade, characterized by unusual genome architecture, appears to be a relevant candidate to serve as a basis for a possible redefinition of the controversial Agrobacterium genus. In this respect, investigating telA in sequenced genomes allows to both ascertain the place of concerned strains into Agrobacterium spp. and their actual assignation to species/genomospecies in this genus.
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France.
Martha H
MH
Ramírez-Bahena
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France.
Ludovic
L
Vial
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France; CNRS, UMR5558, Biométrie et Biologie Evolutive, 69622 Villeurbanne, France; Ecole Normale Supérieure de Lyon, 69342 Lyon, France.
Florent
F
Lassalle
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France.
Benjamin
B
Diel
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France.
David
D
Chapulliot
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5558, Biométrie et Biologie Evolutive, 69622 Villeurbanne, France.
Vincent
V
Daubin
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France. Electronic address: nesme@univ-lyon1.fr.
Xavier
X
Nesme
Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France.
Daniel
D
Muller
D060054:Agrobacterium / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D049810:Genetic Speciation; D016680:Genome, Bacterial / Q000235:genetics; D010802:Phylogeny; D012231:Rhizobium / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D019098:Telomerase / Q000235:genetics*
D019098:Telomerase
Bacterial speciation; Genome architecture; Protelomerase; Species complex; TelA