Structural and functional organization of the plasmid regulons of Rhizobium leguminosarum symbiotic genes

• Published in: Microbiology (New York) Vol. 85; no. 6; pp. 708 - 716
• Main Authors: Chirak, E. R., Kopat’, V. V., Kimeklis, A. K., Safronova, V. I., Belimov, A. A., Chirak, E. L., Tupikin, A. E., Andronov, E. E., Provorov, N. A.
• Format: Journal Article
• Language: English
• Published: Moscow Pleiades Publishing 01-11-2016; Springer Nature B.V
• Subjects: Bacteria; Biomedical and Life Sciences; Experimental Articles; Foraging behavior; Host specificity; Life Sciences; Medical Microbiology; Microbiology; Rhizobium leguminosarum; Symbiosis; evolution of symbiosis; genes; horizontal gene transfer; legume–rhizobia symbiosis
• ISSN: 0026-2617; 1608-3237
• DOI: 10.1134/S0026261716060072

The structure of the plasmid locus containing the
sym
-genes (
nod
-,
nif
-, and
fix
-operons) was investigated in eight
Rhizobium leguminosarum
strains differing in their origin and host specificity, including five strains of the
viciae
biovar—symbionts of pea (3), forage beans (1), and
Vavilovia
(1)—as well as three strains of the biovar
trifolii
(clover symbionts). Strains of
R. leguminosarum
bv.
viciae
, which possess the
nodX
gene (controlling acetylation of the Nod factor, which is responsible for the ability of rhizobia to form symbioses with a broad spectrum of hosts, including the “Afghan” pea lines, homozygous by the allele sym
2A
), are characterized by a less compact location of the
sym
-genes than the strains lacking the
nodX
gene. The size of the symbiotic cluster in the strains possessing
nodX
was 94.5 ± 3.5 kb, with the share of the
sym
-genes of 36.5 ± 1.5%, while for the strains lacking
nodX
these values were 61.7 ± 3.7 kb and 56.3 ± 1.4%, respectively (significant difference at
P
0
< 0.01). Syntenic structures were revealed in the symbiotic regions of strains Vaf12, UPM1131, and TOM, as well as syntenic structures of non-symbiotic regions in strains Vaf12, TOM, and WSM1689. The correlation coefficients between the matrices of genetic distances in the analyzed strains for the
nod
ABC,
nif
HDK, and
fix
ABC operons were on average 0.993 ± 0.002, while their values for the plasmid sites located between the sym-genes were considerably less (0.706 ± 0.010). In these regions, 21 to 27% of the genes were involved in amino acid transport and metabolism, which was substantially higher than the average for the genome of
R. leguminosarum
bv.
viciae
(11–12%). These data suggest that the evolution of
R. leguminosarum
bv.
viciae
, defined by narrowing of the host specificity (associated with a loss of the
nodX
gene), was accompanied by reduction of the regions of plasmids located between the
sym
-genes, as well as by specialization of these areas to perform the functions related to symbiotic nitrogen fixation. The observed increase of density in the cluster of
sym
-genes may be associated with intensification of their horizontal transfer in the populations of rhizobia, which determines the speed of evolution of the symbiotic system.