Transcriptomic Studies of the Effect of nod Gene-Inducing Molecules in Rhizobia: Different Weapons, One Purpose

Jiménez‐Guerrero, Irene; Acosta‐Jurado, Sebastián; Cerro, Pablo del; Navarro‐Gómez, Pilar; López‐Baena, Francisco Javier; Ollero, Francisco Javier; Vinardell, José‐María

doi:10.3390/genes9010001

Cited by 42 publications

(28 citation statements)

References 121 publications

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“…trifolii is a Gram-negative bacterium that exists as a free-living organism in the soil or establishes nitrogen-fixing symbiosis with clover plants ( Trifolium spp.). This microorganism belongs to a large and diverse group of soil bacteria, collectively called rhizobia, which possess the ability to induce nodules on roots and stems of legumes [ 1 , 2 ]. Within nodules, new plant organs ensuring a special ecological niche, rhizobia reduce dinitrogen to ammonia, which is then used by the host plant.…”

Section: Introductionmentioning

confidence: 99%

Mutation in the pssZ Gene Negatively Impacts Exopolysaccharide Synthesis, Surface Properties, and Symbiosis of Rhizobium leguminosarum bv. trifolii with Clover

Lipa

Vinardell

Kopcińska

et al. 2018

Genes

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Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a nitrogen-fixing symbiosis with clover plants (Trifolium spp.). This bacterium secretes large amounts of acidic exopolysaccharide (EPS), which plays an essential role in the symbiotic interaction with the host plant. This polymer is biosynthesized by a multi-enzymatic complex located in the bacterial inner membrane, whose components are encoded by a large chromosomal gene cluster, called Pss-I. In this study, we characterize R. leguminosarum bv. trifolii strain Rt297 that harbors a Tn5 transposon insertion located in the pssZ gene from the Pss-I region. This gene codes for a protein that shares high identity with bacterial serine/threonine protein phosphatases. We demonstrated that the pssZ mutation causes pleiotropic effects in rhizobial cells. Strain Rt297 exhibited several physiological and symbiotic defects, such as lack of EPS production, reduced growth kinetics and motility, altered cell-surface properties, and failure to infect the host plant. These data indicate that the protein encoded by the pssZ gene is indispensable for EPS synthesis, but also required for proper functioning of R. leguminosarum bv. trifolii cells.

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Section: Introductionmentioning

confidence: 99%

Mutation in the pssZ Gene Negatively Impacts Exopolysaccharide Synthesis, Surface Properties, and Symbiosis of Rhizobium leguminosarum bv. trifolii with Clover

Lipa

Vinardell

Kopcińska

et al. 2018

Genes

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“…Recently, the effects of G. max RE on two B. diazoefficiens strains, 4534 and 4222, were analysed by transcriptomics [ 53 ], which showed that several genes coding for two-component systems ( nodW, phyR-σ EcfG ), bacterial chemotaxis ( cheA ), ATP-binding cassette (ABC) transport proteins, and indole-3-acetic acid (IAA) metabolism were upregulated in the more competitive B. diazoefficiens strain 4534. A recent publication of Jiménez-Guerrero and colleagues extensively reviewed the transcriptomic studies performed in alpha-rhizobia with an emphasis on the effect of flavonoids on the activation of nod genes [ 98 ].…”

Section: Functional Genomics Of Rhizobia-legume Symbiosismentioning

confidence: 99%

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia

Lardi

Pessi

2018

High-Throughput

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Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

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“…The molecular mechanisms underlying the physiological adaptation of rhizobia in the root nodules have so far been mainly studied in α-rhizobial symbiosis model systems. Several studies have relied on functional genomics technologies like transcriptomics, proteomics and metabolomics, and comparative genomics [11,12,13,14,15,16,17,18,19,20]. …”

Section: Introductionmentioning

confidence: 99%

Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris

Lardi

Liu

Giudice

et al. 2018

IJMS

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RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T formed root nodules on Phaseolus vulgaris cv. Negro jamapa, which were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by a P. phymatum rpoN Fix− mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix− and Fix+ nodules—combined with a search for RpoN binding sequences in promoter regions of regulated genes—confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also allowed us to identify additional target genes, whose differential expression was able to explain the observed metabolite changes in numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant, and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype, as fewer but heavier nodules were formed on P. vulgaris roots.

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Transcriptomic Studies of the Effect of nod Gene-Inducing Molecules in Rhizobia: Different Weapons, One Purpose

Cited by 42 publications

References 121 publications

Mutation in the pssZ Gene Negatively Impacts Exopolysaccharide Synthesis, Surface Properties, and Symbiosis of Rhizobium leguminosarum bv. trifolii with Clover

Mutation in the pssZ Gene Negatively Impacts Exopolysaccharide Synthesis, Surface Properties, and Symbiosis of Rhizobium leguminosarum bv. trifolii with Clover

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia

Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris

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