Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus

Abstract

Research on legume nodule metabolism has contributed greatly to our knowledge of primary carbon and nitrogen metabolism in plants in general, and in symbiotic nitrogen fixation in particular. However, most previous studies focused on one or a few genes/enzymes involved in selected metabolic pathways in many different legume species. We utilized the tools of transcriptomics and metabolomics to obtain an unprecedented overview of the metabolic differentiation that results from nodule development in the model legume, Lotus japonicus. Using an array of more than 5000 nodule cDNA clones, representing 2500 different genes, we identified approximately 860 genes that were more highly expressed in nodules than in roots. One-third of these are involved in metabolism and transport, and over 100 encode proteins that are likely to be involved in signalling, or regulation of gene expression at the transcriptional or post-transcriptional level. Several metabolic pathways appeared to be co-ordinately upregulated in nodules, including glycolysis, CO(2) fixation, amino acid biosynthesis, and purine, haem, and redox metabolism. Insight into the physiological conditions that prevail within nodules was obtained from specific sets of induced genes. In addition to the expected signs of hypoxia, numerous indications were obtained that nodule cells also experience P-limitation and osmotic stress. Several potential regulators of these stress responses were identified. Metabolite profiling by gas chromatography coupled to mass spectrometry revealed a distinct metabolic phenotype for nodules that reflected the global changes in metabolism inferred from transcriptome analysis.

Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade

“…During the switch from a root-specific to a nodule-specific gene expression program, important transcriptional changes would be expected to accompany bacterial recognition and invasion and plant morphological changes. This situation is extremely close to that described in different model legume transcriptomic studies (Asamizu et al, 2000;Journet et al, 2002;Colebatch et al, 2004;El Yahyaoui et al, 2004;Maunoury et al, 2010) with upregulation of DCAT, a dicarboxylate transporter for delivery of photosynthates as TCA intermediates to the symbiont and a Gln synthetase, homolog of early nodulin M. truncatula N6 (Mathis et al, 1999), for assimilation of the ammonium fixed and transferred to the plant cytosol, which is consistent with previous demonstrations that the assimilation of 13 N was through Gln synthetase synthesizing Gln (Lundberg and Lundquist, 2004). The level of expression of several defense genes (defensins, chitinases) as well as stress proteins (catalase, DnaJ, Mdr) was also modified in a similar way to what is known to occur in legume nodules (Pucciariello et al, 2009;Maunoury et al, 2010), in particular a g-expansin natriuretic peptide that belongs to a novel class of peptide signal molecules (plant natriuretic peptides) involved in the response to biotic and abiotic stresses (Gottig et al, 2008;Meier et al, 2008).…”

“…2). The distribution into functional categories was found to be very close to that observed for the unigene sets and thus confirmed high metabolism and transport activity regulation during nodule formation (Journet et al, 2002;Colebatch et al, 2004;El Yahyaoui et al, 2004). Due to the small number of regulated genes, some categories, like "ubiquitin cycle," "cell communication," and "DNA metabolic process," were not represented.…”

Ascorbate oxidase: The unexpected involvement of a ‘wasteful enzyme’ in the symbioses with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi

“…A cDNA array experiment using 9652 nodule-derived EST clones spotted on a nylon membrane identified several genes induced upon rhizobial inoculation [17], [18] and [19]. Among them, the clone LjNEST98c11r (Genbank accession CB829448) was identified, which was transcriptionally induced during nodule development.…”

Peace Talks and Trade Deals. Keys to Long-Term Harmony in Legume-Microbe Symbioses

“…While compatible solutes may not be a currency of trade between legumes and rhizobia, induction of plant genes involved in polyamine, polyol, and Pro synthesis indicate that nodule cells may have to work overtime for osmotic homeostasis (Colebatch et al, 2004). Of more interest from the point of view of trade between host and microsymbionts is the growing list of nodule-induced plant genes encoding transporters (Colebatch et al, 2004;El Yahyaoui et al, 2004;Kouchi et al, 2004), some of which appear to be located on the symbiosome membrane, based on proteomics data (Saalbach et al, 2002;Wienkoop and Saalbach, 2003;Catalano et al, 2004). The symbiosome membrane is the specialized plant membrane that separates bacteroids from the host cell cytoplasm and controls the traffic of nutrients between the two.…”

“…Transcriptomics and proteomics are beginning to reveal the true extent of plant and bacterial differentiation during nodule development. Hundreds of novel plant genes that are either induced or repressed during nodule development have now been identified using cDNA arrays (Colebatch et al, 2002(Colebatch et al, , 2004El Yahyaoui et al, 2004;Kouchi et al, 2004;Kuster et al, 2004;Lee et al, 2004), oligonucleotide microarrays (Mitra et al, 2004b), and bioinformatic approaches (Fedorova et al, 2002;Journet et al, 2002). Many of these are involved in metabolism and transport (Colebatch et al, 2004;El Yahyaoui et al, 2004;Kouchi et al, 2004).…”