Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

被引：77

作者：

Galardini, Marco ^{[1
]}

Mengoni, Alessio ^{[1
]}

Brilli, Matteo ^{[2
]}

Pini, Francesco ^{[1
]}

Fioravanti, Antonella ^{[1
]}

Lucas, Susan ^{[3
]}

Lapidus, Alla ^{[4
]}

Cheng, Jan-Fang ^{[3
]}

Goodwin, Lynne ^{[5
]}

Pitluck, Samuel ^{[3
]}

Land, Miriam ^{[6
]}

Hauser, Loren ^{[6
]}

Woike, Tanja ^{[3
]}

Mikhailova, Natalia ^{[3
]}

Ivanova, Natalia ^{[3
]}

Daligault, Hajnalka ^{[3
]}

Bruce, David ^{[3
]}

Detter, Chris ^{[3
]}

Tapia, Roxanne ^{[3
]}

Han, Cliff ^{[3
]}

Teshima, Hazuki ^{[3
]}

Mocali, Stefano ^{[7
]}

Bazzicalupo, Marco ^{[1
]}

Biondi, Emanuele G. ^{[1
,8
]}

机构：

[1] Univ Florence, Dept Evolutionary Biol, I-50125 Florence, Italy

[2] Univ Lyon 1, CNRS, Lab Biometrie & Biol Evolut, UMR 5558, F-69365 Lyon, France

[3] Joint Genome Inst, DOE, Walnut Creek, CA USA

[4] Fox Chase Canc Ctr, Philadelphia, PA 19111 USA

[5] Los Alamos Natl Lab, Los Alamos, NM USA

[6] Oak Ridge Natl Lab, Oak Ridge, TN USA

[7] Agrobiol & Pedol Ctr ABP, Agr Res Council, I-50121 Florence, Italy

[8] CNRS, Interdisciplinary Res Inst, Villenenuve Dascq, France

来源：

BMC GENOMICS | 2011年 / 12卷

关键词：

Sinorhizobium meliloti nodulation; symbiosis; comparative genomics; pangenome; panregulon; RHIZOBIUM-MELILOTI; COMPARATIVE GENOMICS; SEQUENCE-ANALYSIS; GENES; IDENTIFICATION; BIOSYNTHESIS; RECOGNITION; EXPRESSION; REGULATOR; ORTHOLOGS;

D O I：

10.1186/1471-2164-12-235

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Background: Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. Results: With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. Conclusions: In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

引用

页数：15

共 69 条

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