Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58

Bazzicalupo, Marco; Biondi, Emanuele G.; Brambilla, Eveline; Brilli, Matteo; Bruce, David; Chain, Patrick; Chen, Amy; Daligault, Hajnalka; Davenport, Karen W.; Deshpande, Shweta; Detter, John C.; Goodwin, Lynne; Han, Cliff; Han, James; Ivanova, Natalia; Klenk, Hans‐Peter; Kyrpides, Nikos C.; Markowitz, Victor; Mavrommatis, Konstantinos; Mocali, Stefano; Nolan, Matt; Pagani, Ioanna; Pati, Amrita; Pini, Francesco; Pitluck, Sam; Spini, Giulia; Szeto, Ernest; Teshima, Hazuki; Woyke, Tanja; Mengoni, Alessio

doi:10.4056/sigs.3797438

Cited by 8 publications

(12 citation statements)

References 25 publications

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“…However, several strains of these rhizobial species do not possess the ability to induce nodule formation (van Rhijn and Vanderleyden, 1995). Probably due to this heterogeneous life style (both free-living and symbiont) rhizobia have large genomes, often composed by several replicative elements (a chromosome, plus additional elements as chromids, megaplasmids, or plasmids) (Harrison et al, 2010;Pini et al, 2011;Black et al, 2012;Galardini et al, 2013a).…”

Section: Rhizobium Genetic Resources Host Specificity and Diversitymentioning

confidence: 99%

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

Dwivedi

Sahrawat

Upadhyaya

et al. 2015

Advances in Agronomy

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This chapter was originally published in the book Advances in Agronomy. The copy attached is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research, and educational use. This includes without limitation use in instruction at your institution, distribution to specific colleagues, and providing a copy to your institution's administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution's website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier's

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Section: Rhizobium Genetic Resources Host Specificity and Diversitymentioning

confidence: 99%

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

Dwivedi

Sahrawat

Upadhyaya

et al. 2015

Advances in Agronomy

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“…Recent reports have shown that there are only two genes essential for growth in minimal media and soil encoded in the S. meliloti chromid [ 32 ], even though the chromid harbours many genes shared by all sequenced strains of S. meliloti species. Moreover, S. meliloti has several genomes sequenced to date [ 23 , 30 , 33 – 39 ] and the potential for biotechnological and agricultural applications, which could benefit from this analysis. At the comparative genomics level, different strains show quite a high level of variation.…”

Section: Introductionmentioning

confidence: 99%

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

et al. 2015

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Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes.

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“…The sequence of the S. meliloti AK21 genome has not yet been published, albeit Eckhardt lysis analysis revealed the presence of four replicons, three large ones probably corresponding to the chromosome, pSymA and pSymB, and a 120 kb-length plasmid (Ibragimova et al 2006 ; M. Bazzicalupo personal communication). It is known that other sequenced strains of S. meliloti present a genomic organization similar to Rm1021 (Galardini et al 2011 ) which was annotated with 6,292 genes distributed in the three replicons: 3,429 genes in the chromosome; 1,293 genes in pSymA; and 1,570 genes in pSymB (Galibert et al 2001 ). We detected 365 protein-coding genes differing between the two strains (equivalent to 5.8% of the annotated Rm1021 genome, Additional file 1 ), most of which were absent from or markedly different in S. meliloti AK21, with only one of these genes displaying a lower signal intensity in Rm1021 (SMa1073, 89% identity to an ATP-binding protein).…”

Section: Resultsmentioning

confidence: 99%

“…S. meliloti is found in many different soil environments around the world, suggesting that this species has broad metabolic adaptation capabilities (Souza et al 1992 ; Paffetti et al 1996 ; Jebara et al 2001 ; Roumiantseva et al 2002 ; Biondi et al 2003 ; Giuntini et al 2005 ; Bailly et al 2007 ; Jones et al 2007 ; Stiens et al 2008 ; Schneiker-Bekel et al 2011 ). Investigations of genome dynamics have been carried out at the intra- and interspecies levels in recent years in intensive studies of natural isolates of related rhizobia, discriminating between core and accessory genes (Guo et al 2009 ; Galardini et al 2011 , 2013a , b ; Bailly et al 2011 ; Epstein et al 2012 ; Sugawara et al 2013 ). The complete annotated genome sequence of S. meliloti isolated from diverse soil types (agricultural fields, contaminated soils,…) and continents (1021, SM11, BL225C, AK83, GR4, Rm41) can now be obtained from databases (Galibert et al 2001 ; Schneiker-Bekel et al 2011 ; Galardini et al 2011 ; Martínez-Abarca et al 2013 ), and several other draft genomes are also available (Galardini et al 2013a , b ).…”

Section: Introductionmentioning

confidence: 99%

“…Investigations of genome dynamics have been carried out at the intra- and interspecies levels in recent years in intensive studies of natural isolates of related rhizobia, discriminating between core and accessory genes (Guo et al 2009 ; Galardini et al 2011 , 2013a , b ; Bailly et al 2011 ; Epstein et al 2012 ; Sugawara et al 2013 ). The complete annotated genome sequence of S. meliloti isolated from diverse soil types (agricultural fields, contaminated soils,…) and continents (1021, SM11, BL225C, AK83, GR4, Rm41) can now be obtained from databases (Galibert et al 2001 ; Schneiker-Bekel et al 2011 ; Galardini et al 2011 ; Martínez-Abarca et al 2013 ), and several other draft genomes are also available (Galardini et al 2013a , b ).…”

Section: Introductionmentioning

confidence: 99%

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Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region

et al. 2015

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The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. S. meliloti AK21 is a wild type strain that forms nodules on Medicago plants in saline and drought conditions in the Aral Sea Region. The aim of this work was to establish the genetic similarities and differences between S. meliloti AK21 and the reference strain S. meliloti 1021. Comparative genome hybridization with the model reference strain S. meliloti 1021 yielded 365 variable genes, grouped into 11 regions in the three main replicons in S. meliloti AK21. The most extensive regions of variability were found in the symbiotic plasmid pSymA, which also contained the largest number of orthologous and polymorphic sequences identified by suppression subtractive hybridization. This procedure identified a large number of divergent sequences and others without homology in the databases, the further investigation of which could provide new insight into the alternative metabolic pathways present in S. meliloti AK21. We identified a plasmid replication module from the repABC replicon family, together with plasmid mobilization-related genes (traG and a VirB9-like protein), which suggest that this indigenous isolate harbors an accessory plasmid. Furthermore, the transcriptomic profiles reflected differences in gene content and regulation between S. meliloti AK21 and S. meliloti 1021 (ExpR and PhoB regulons), but provided evidence for an as yet unknown, alternative mechanism involving activation of the cbb3 terminal oxidase. Finally, phenotypic microarrays characterization revealed a greater versatility of substrate use and chemical degradation than for S. meliloti 1021.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1062-z) contains supplementary material, which is available to authorized users.

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Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58

Cited by 8 publications

References 25 publications

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region

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