IN INOCULANTS Nodulaid - 17th International Nitrogen Fixation ...
IN INOCULANTS Nodulaid - 17th International Nitrogen Fixation ... IN INOCULANTS Nodulaid - 17th International Nitrogen Fixation ...
17 th International Congress on Nitrogen Fixation Fremantle, Western Australia 27 November – 1 December 2011 Session Details: Tuesday 29 November 2011 Plenary Session 3 0900 - 1030 Authors: Philip Poole, Graham Hood, Alison East, Ramakrishnan Karunakaran, Vinoy Ramachandran, Jurgen Prell John Innes Centre, Norwich UK Presentation Title: Metabolic transitions of Rhizobium from rhizosphere to bacteroid Presentation Time: 1000 - 1030 Comparative transcriptomics has been used to examine the changes when Rhizobium leguminosarum grows in the pea, alfalfa or sugar beet rhizospheres. This enabled the identification of genes that are expressed generally in the rhizosphere, as well as those that are legume (pea or alfalfa) or host (pea) specific. Carbon metabolism by bacteria in the rhizosphere all plants is dominated by organic acids with particularly strong induction of C1 and C2 metabolism. Gluconeogenesis is induced, indicating that while sugars are present, they are only minor carbon sources relative to the organic acids. Aromatic amino acids such as phenylalanine also appear to be particularly important. As expected nod genes were induced in the pea and alfalfa rhizosphere but not in the rhizosphere of sugar beet. Next we examined gene expression in early (7 d nodules) and mature bacteroids (15- 28 d nodules). This enabled gene expression to be partitioned into developmental stages from the rhizosphere, probably infection thread/early development and mature bacteroids. Genes induced in infection threads and early development include; metal accumulation, oxidative stress and export systems for probable plant metabolites, GABA catabolism and a new terminal oxidase. To obtain a clear picture of genes induced in infection threads and early development it was crucial to subtract genes already induced in the rhizosphere. Bacteroid metabolism is characterized by dicarboxylate oxidation with very high expression of the decarboxylating arm of the TCAcycle. Amino acid synthesis is bacteroids is shut down with transcriptional as well as metabolite analysis showing almost all pools of amino acids have collapsed in bacteroids. This leads to amino acid auxotrophy for branched chain amino acids in pea and bean as demonstrated by a dependence on the Aap and Bra transporters. However, alfalfa bacteroids mutated in Aap and Bra still fix nitrogen so either they have an alternative transport system for branched chain amino acids or they retain synthesis of these amino acids. 36 2011
17 th International Congress on Nitrogen Fixation Fremantle, Western Australia 27 November – 1 December 2011 Session Details: Tuesday 29 November 2011 Authors: Concurrent Session 4 – Applications of New Technologies 1100 - 1230 Brice Roux 1 , Erika Sallet 1 , Nathalie Rodde 1 , Laurent Sauviac 1 , Olivier Catrice 1 ,Ton Timmers 1 , Thomas Faraut 2 , Thomas Schiex 3 , Françoise Jardinaud 1 , Fernanda de Carvalho-Niebel 1 , Frédéric Debéllé 1 , Delphine Capela 1 , Claude Bruand 1 , Jérôme Gouzy 1 , Pascal Gamas 1 1 . Laboratoire des Interactions Plantes Microorganismes (LIPM) CNRS-INRA, Chemin de borde rouge BP 52627, 31326 Castanet-Tolosan cedex, France. 2 . INRA LGC Chemin de Borde Rouge BP52627, 31326 Castanet-Tolosan cedex, France. 3 . INRA UBIA Chemin de Borde Rouge BP52627, 31326 Castanet-Tolosan cedex, France. Presentation Title: Molecular dissection of the rhizobium-legume interaction by RNA seq and laser microdissection approaches Presentation Time: 1100 - 1120 In order to have a comprehensive view of the genes involved in the symbiotic rhizobium-legume interaction, we set up integrated methods for simultaneous gene expression profiling of both partners, based upon RNA seq approaches. We analysed the plant and bacterial transcriptomes of whole and laser micro-dissected root nodules and compared them to transcriptomes from non inoculated roots or bacterial cultures, using Sinorhizobium meliloti 2011-Medicago truncatula as a model system. We thus combined genome-wide, quantitative and sensitive analyses of gene expression with technologies enabling tissue-level resolution. Importantly, we chose strand-specific RNA seq techniques that allowed us to identify, in addition to protein coding mRNAs, bacterial and plant short and long non-coding RNAs (ncRNAs), not previously predicted by automatic genome annotation. To provide a solid framework for quantitative transcriptome analyses, we sequenced and (re)annotated the genome of S. meliloti strain 2011. To do so, we developed bioinformatics tools for bacterial gene prediction that notably take advantage of RNA seq data. The results were validated by visual inspection and completed by manual annotation. We also completed the currently available M. truncatula genome sequence data by high depth Illumina sequencing. We thus found many bacterial ncRNAs previously described in other groups by different experimental approaches, which fully validated our approaches. We also discovered additional bacterial ncRNAs, as well as many plant ncRNAs (such as antisense RNAs), a number of which are differentially regulated when comparing roots and nodules. We are now using this extensive set of tools and data to (re)examine the sets of proteincoding and non coding genes involved in early and late stages of the rhizobium-legume interaction. 37 2011
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17 th <strong>International</strong> Congress on <strong>Nitrogen</strong> <strong>Fixation</strong><br />
Fremantle, Western Australia<br />
27 November – 1 December 2011<br />
Session Details: Tuesday 29 November 2011<br />
Plenary Session 3<br />
0900 - 1030<br />
Authors: Philip Poole, Graham Hood, Alison East, Ramakrishnan Karunakaran, Vinoy<br />
Ramachandran, Jurgen Prell<br />
John Innes Centre, Norwich UK<br />
Presentation Title: Metabolic transitions of Rhizobium from rhizosphere to bacteroid<br />
Presentation Time: 1000 - 1030<br />
Comparative transcriptomics has been used to examine the changes when Rhizobium leguminosarum grows in<br />
the pea, alfalfa or sugar beet rhizospheres. This enabled the identification of genes that are expressed generally<br />
in the rhizosphere, as well as those that are legume (pea or alfalfa) or host (pea) specific. Carbon metabolism by<br />
bacteria in the rhizosphere all plants is dominated by organic acids with particularly strong induction of C1 and<br />
C2 metabolism. Gluconeogenesis is induced, indicating that while sugars are present, they are only minor<br />
carbon sources relative to the organic acids. Aromatic amino acids such as phenylalanine also appear to be<br />
particularly important. As expected nod genes were induced in the pea and alfalfa rhizosphere but not in the<br />
rhizosphere of sugar beet. Next we examined gene expression in early (7 d nodules) and mature bacteroids (15-<br />
28 d nodules). This enabled gene expression to be partitioned into developmental stages from the rhizosphere,<br />
probably infection thread/early development and mature bacteroids. Genes induced in infection threads and early<br />
development include; metal accumulation, oxidative stress and export systems for probable plant metabolites,<br />
GABA catabolism and a new terminal oxidase. To obtain a clear picture of genes induced in infection threads<br />
and early development it was crucial to subtract genes already induced in the rhizosphere. Bacteroid metabolism<br />
is characterized by dicarboxylate oxidation with very high expression of the decarboxylating arm of the TCAcycle.<br />
Amino acid synthesis is bacteroids is shut down with transcriptional as well as metabolite analysis showing<br />
almost all pools of amino acids have collapsed in bacteroids. This leads to amino acid auxotrophy for branched<br />
chain amino acids in pea and bean as demonstrated by a dependence on the Aap and Bra transporters.<br />
However, alfalfa bacteroids mutated in Aap and Bra still fix nitrogen so either they have an alternative transport<br />
system for branched chain amino acids or they retain synthesis of these amino acids.<br />
36<br />
2011
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