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

Abstract

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 insidemore » 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.« less

Authors:
 [1];  [1];  [2];  [1];  [1];  [3];  [3];  [3];  [4];  [3];  [5];  [5];  [3];  [3];  [3];  [4];  [4];  [3];  [4];  [4] more »;  [4];  [6];  [1];  [1] « less
  1. University of Florence
  2. Universite de Lyon, France
  3. U.S. Department of Energy, Joint Genome Institute
  4. Los Alamos National Laboratory (LANL)
  5. ORNL
  6. Agrobiol & Pedol Ctr ABP, Agr Res Council, I-50121 Florence, Italy
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
Work for Others (WFO)
OSTI Identifier:
1020816
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: BMC Genomics; Journal Volume: 12; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; DIVERSIFICATION; GENES; GENETICS; NITROGEN FIXATION; PLANT GROWTH; PLASMIDS; REPLICONS; STRAINS; SYMBIOSIS; TRANSCRIPTION FACTORS; RHIZOBIUM-LEGUMINOSARUM; COMPARATIVE GENOMICS; SEQUENCE-ANALYSIS; PAN-GENOME; NODULATION; IDENTIFICATION; BIOSYNTHESIS; RECOGNITION; TRANSPORTER

Citation Formats

Galardini, Marco, Mengoni, Alessio, Brilli, Matteo, Pini, Francesco, Fioravanti, Antonella, Lucas, Susan, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Land, Miriam L, Hauser, Loren John, Woyke, Tanja, Mikhailova, Natalia, Ivanova, N, Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Teshima, Hazuki, Mocali, Stefano, Bazzicalupo, Marco, and Biondi, Emanuele. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. United States: N. p., 2011. Web. doi:10.1186/1471-2164-12-235.
Galardini, Marco, Mengoni, Alessio, Brilli, Matteo, Pini, Francesco, Fioravanti, Antonella, Lucas, Susan, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Land, Miriam L, Hauser, Loren John, Woyke, Tanja, Mikhailova, Natalia, Ivanova, N, Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Teshima, Hazuki, Mocali, Stefano, Bazzicalupo, Marco, & Biondi, Emanuele. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. United States. doi:10.1186/1471-2164-12-235.
Galardini, Marco, Mengoni, Alessio, Brilli, Matteo, Pini, Francesco, Fioravanti, Antonella, Lucas, Susan, Lapidus, Alla L., Cheng, Jan-Fang, Goodwin, Lynne A., Pitluck, Sam, Land, Miriam L, Hauser, Loren John, Woyke, Tanja, Mikhailova, Natalia, Ivanova, N, Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Teshima, Hazuki, Mocali, Stefano, Bazzicalupo, Marco, and Biondi, Emanuele. Sat . "Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti". United States. doi:10.1186/1471-2164-12-235.
@article{osti_1020816,
title = {Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti},
author = {Galardini, Marco and Mengoni, Alessio and Brilli, Matteo and Pini, Francesco and Fioravanti, Antonella and Lucas, Susan and Lapidus, Alla L. and Cheng, Jan-Fang and Goodwin, Lynne A. and Pitluck, Sam and Land, Miriam L and Hauser, Loren John and Woyke, Tanja and Mikhailova, Natalia and Ivanova, N and Daligault, Hajnalka E. and Bruce, David and Detter, J. Chris and Tapia, Roxanne and Han, Cliff and Teshima, Hazuki and Mocali, Stefano and Bazzicalupo, Marco and Biondi, Emanuele},
abstractNote = {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.},
doi = {10.1186/1471-2164-12-235},
journal = {BMC Genomics},
number = 1,
volume = 12,
place = {United States},
year = {Sat Jan 01 00:00:00 EST 2011},
month = {Sat Jan 01 00:00:00 EST 2011}
}
  • Bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. While both the nitrogen stress response (NSR) and phosphate stress response (PSR) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in Sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. The PII proteins, GlnB and GlnK, regulate the NSR activity, but analysis of global transcription changes in a PII deficient mutant suggest that the S. meliloti PII proteins may also regulate the PSR. PII double deletion mutants grow verymore » slowly and pseudoreversion of the slow growth phenotype is common. In order to understand this phenomenon better, transposon mutants were isolated that had a faster growing phenotype. One mutation was in phoB, the response regulator for a two component regulatory system that is important in the PSR. phoB::Tn5 mutants had different phenotypes in the wild type compared to a PII deficient background. This led to the hypothesis that phosphate stress affects the NSR and conversely, that nitrogen stress affects the PSR. These results show that phosphate availability affects glutamine synthetase activity and expression, which are often used as indicators of NSR activity, but that nitrogen availability did not affect alkaline phosphatase activity and expression, which are indicators of PSR activity. Finally, we conclude that the NSR is co-regulated by nitrogen and phosphate, whereas the PSR does not appear to be co-regulated by nitrogen in addition to its known phosphate regulation.« less
  • Symbiotic nitrogen fixation (SNF) between rhizobia and legumes requires metabolic coordination within specialized root organs called nodules. Nodules formed in the symbiosis between S. medicae and barrel medic (M. truncatula) are indeterminate, cylindrical, and contain spatially distinct developmental zones. Bacteria in the infection zone II (ZII), interzone II-III (IZ), and nitrogen fixation zone III (ZIII) represent different stages in the metabolic progression from free-living bacteria into nitrogen fixing bacteroids. To better understand the coordination of plant and bacterial metabolism within the nodule, we used liquid and gas chromatography coupled to tandem mass spectrometry (MS) to observe protein and metabolite profilesmore » representative of ZII, IZ, ZIII, whole-nodule, and primary root. Our MS-based approach confidently identified 361 S. medicae proteins and 888 M. truncatula proteins, as well as 160 metabolites from each tissue. The data are consistent with several organ- and zone-specific protein and metabolite localization patterns characterized previously. Here, we used our comprehensive dataset to demonstrate how multiple branches of primary metabolism are coordinated between symbionts and zones, including central carbon, fatty acid, and amino acid metabolism. For example, M. truncatula glycolysis enzymes accumulate from zone I to zone III within the nodule, while equivalent S. medicae enzymes decrease in abundance. We also show the localization of S. medicae's transition to dicarboxylic acid-dependent carbon metabolism within the IZ. The spatial abundance patterns of S. medicae fatty acid (FA) biosynthesis enzymes indicate an increased demand for FA production in the IZ and ZIII as compared to ZI. Our observations provide a resource for those seeking to understand coordinated physiological changes during the development of SNF.« less
  • Symbiotic nitrogen fixation (SNF) between rhizobia and legumes requires metabolic coordination within specialized root organs called nodules. Nodules formed in the symbiosis between S. medicae and barrel medic (M. truncatula) are indeterminate, cylindrical, and contain spatially distinct developmental zones. Bacteria in the infection zone II (ZII), interzone II-III (IZ), and nitrogen fixation zone III (ZIII) represent different stages in the metabolic progression from free-living bacteria into nitrogen fixing bacteroids. To better understand the coordination of plant and bacterial metabolism within the nodule, we used liquid and gas chromatography coupled to tandem mass spectrometry (MS) to observe protein and metabolite profilesmore » representative of ZII, IZ, ZIII, whole-nodule, and primary root. Our MS-based approach confidently identified 361 S. medicae proteins and 888 M. truncatula proteins, as well as 160 metabolites from each tissue. The data are consistent with several organ- and zone-specific protein and metabolite localization patterns characterized previously. Here, we used our comprehensive dataset to demonstrate how multiple branches of primary metabolism are coordinated between symbionts and zones, including central carbon, fatty acid, and amino acid metabolism. For example, M. truncatula glycolysis enzymes accumulate from zone I to zone III within the nodule, while equivalent S. medicae enzymes decrease in abundance. We also show the localization of S. medicae's transition to dicarboxylic acid-dependent carbon metabolism within the IZ. The spatial abundance patterns of S. medicae fatty acid (FA) biosynthesis enzymes indicate an increased demand for FA production in the IZ and ZIII as compared to ZI. Our observations provide a resource for those seeking to understand coordinated physiological changes during the development of SNF.« less
  • Lipopolysaccharides (LPS) and capsular polysaccharides (K antigens) may influence the interaction of rhizobia with their specific hosts; therefore, the authors conducted a comparative analysis of Sinorhizobium fredii and Sinorhizobium meliloti, which are genetically related, yet symbiotically distinct, nitrogen-fixing microsymbionts of legumes. They found that both species typically produce strain-specific K antigens that consist of 3-deoxy-D-manno-2-octulosonic acid (Kdo), or other 1-carboxy-2-keto-3-deoxy sugars (such as sialic acid), and hexoses. The K antigens of each strain are distinguished by glycosyl composition, anomeric configuration, acetylation, and molecular weight distribution. One consistent difference between the K antigens of S. fredii and those of S. melilotimore » is the presence of N-acetyl groups in the polysaccharides of the latter. In contrast to the K antigens, the LPS of Sinorhizobium spp. are major common antigens. Rough (R) LPS is the predominant form of LPS produced by cultured cells, and some strains release almost no detectable smooth (S) LPS upon extraction. Sinorhizobium spp. are delineated into two major RLPS core serogroups, which do not correspond to species. The O antigens of the SLPS, when present, have similar degrees of polymerization and appear to be structurally conserved throughout the genus. Interestingly, one strain was found to be distinct from all others: S. fredii HH303 produces a unique K antigen, which contains galacturonic acid and rhamnose, and the RLPS did not fall into either of the RLPS core serogroups. The results of this study indicate that the conserved S- and RLPS of Sinorhizobium spp. lack the structural information necessary to influence host specificity, whereas the variable K antigens may affect strain-cultivar interactions.« less
  • The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Angstroms resolution using synchrotron radiation and belonged to the orthorhombic space group C2221, with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Angstroms.