The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments.
BACKGROUND
Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symbiotic genome compartments (SGCs), it is necessary to analyze their common genetic content and organization as well as to study their differences. To date, five SGCs belonging to distinct species of rhizobia have been entirely sequenced. We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available.


RESULTS
The symbiotic plasmid is a circular molecule of 371,255 base-pairs containing 359 coding sequences. Nodulation and nitrogen-fixation genes common to other rhizobia are clustered in a region of 125 kilobases. Numerous sequences related to mobile elements are scattered throughout. In some cases the mobile elements flank blocks of functionally related sequences, thereby suggesting a role in transposition. The plasmid contains 12 reiterated DNA families that are likely to participate in genomic rearrangements. Comparisons between this plasmid and complete rhizobial genomes and symbiotic compartments already sequenced show a general lack of synteny and colinearity, with the exception of some transcriptional units. There are only 20 symbiotic genes that are shared by all SGCs.


CONCLUSIONS
Our data support the notion that the symbiotic compartments of rhizobia genomes are mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition.
González
Víctor
V
Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210.
Bustos
Patricia
P
Ramírez-Romero
Miguel A
MA
Medrano-Soto
Arturo
A
Salgado
Heladia
H
Hernández-González
Ismael
I
Hernández-Celis
Juan Carlos
JC
Quintero
Verónica
V
Moreno-Hagelsieb
Gabriel
G
Girard
Lourdes
L
Rodríguez
Oscar
O
Flores
Margarita
M
Cevallos
Miguel A
MA
Collado-Vides
Julio
J
Romero
David
D
Dávila
Guillermo
G
D000693:Anaerobiosis / Q000502:physiology; D001426:Bacterial Proteins / Q000502:physiology; D001693:Biological Transport, Active / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases / Q000502:physiology; D004735:Energy Transfer / Q000235:genetics; D005420:Flavoproteins / Q000502:physiology; D023061:Gene Order / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics / Q000502:physiology; D016680:Genome, Bacterial; D046911:Macromolecular Substances; D009030:Mosaicism / Q000235:genetics*; D009586:Nitrogen Fixation / Q000235:genetics; D010957:Plasmids / Q000235:genetics*; D051877:RNA Polymerase Sigma 54; D012231:Rhizobium / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012808:Sigma Factor / Q000502:physiology; D013559:Symbiosis / Q000235:genetics*; D026801:Synteny / Q000235:genetics
D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D005420:Flavoproteins; D046911:Macromolecular Substances; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54