From Intracellular Bacteria to Differentiated Bacteroids

Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant

Florian Lamouche, Anaïs Chaumeret, Ibtissem Guefrachi, Quentin Barrière, Olivier Pierre, Florence Guérard, Françoise Gilard, Eric Giraud, Yves Dessaux, Bertrand Gakière, Tatiana Timchenko, A. Kereszt, Peter Mergaert, Benoit Alunni

Research output: Contribution to journalArticle

Abstract

Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.

Original languageEnglish
JournalJournal of bacteriology
Volume201
Issue number17
DOIs
Publication statusPublished - Sep 1 2019

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Bradyrhizobium
Rhizobium
Metabolome
Gene Expression Profiling
Nitrogen
Fabaceae
Bacteria
Symbiosis
Transcriptome
Bacterial Physiological Phenomena
Soil
Nitrogen Cycle
Endoreduplication
Cell Enlargement
Polyploidy
Metabolomics
Fertilizers
Plant Cells
Gene Expression Regulation
Life Cycle Stages

Keywords

  • BclA ABC transporter
  • legume-rhizobium symbiosis
  • metabolome
  • terminal bacteroid differentiation
  • transcriptome

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

From Intracellular Bacteria to Differentiated Bacteroids : Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant. / Lamouche, Florian; Chaumeret, Anaïs; Guefrachi, Ibtissem; Barrière, Quentin; Pierre, Olivier; Guérard, Florence; Gilard, Françoise; Giraud, Eric; Dessaux, Yves; Gakière, Bertrand; Timchenko, Tatiana; Kereszt, A.; Mergaert, Peter; Alunni, Benoit.

In: Journal of bacteriology, Vol. 201, No. 17, 01.09.2019.

Research output: Contribution to journalArticle

Lamouche, F, Chaumeret, A, Guefrachi, I, Barrière, Q, Pierre, O, Guérard, F, Gilard, F, Giraud, E, Dessaux, Y, Gakière, B, Timchenko, T, Kereszt, A, Mergaert, P & Alunni, B 2019, 'From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant', Journal of bacteriology, vol. 201, no. 17. https://doi.org/10.1128/JB.00191-19
Lamouche, Florian ; Chaumeret, Anaïs ; Guefrachi, Ibtissem ; Barrière, Quentin ; Pierre, Olivier ; Guérard, Florence ; Gilard, Françoise ; Giraud, Eric ; Dessaux, Yves ; Gakière, Bertrand ; Timchenko, Tatiana ; Kereszt, A. ; Mergaert, Peter ; Alunni, Benoit. / From Intracellular Bacteria to Differentiated Bacteroids : Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant. In: Journal of bacteriology. 2019 ; Vol. 201, No. 17.
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AU - Chaumeret, Anaïs

AU - Guefrachi, Ibtissem

AU - Barrière, Quentin

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AU - Guérard, Florence

AU - Gilard, Françoise

AU - Giraud, Eric

AU - Dessaux, Yves

AU - Gakière, Bertrand

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