Large-Scale Analysis of Gene Expression Profiles during Early Stages of Root Nodule Formation in a Model Legume, Lotus japonicus

Abstract

Gene expression profiles during early stages of formation of symbiotic nitrogen-fixing nodules in a model legume Lotus japonicus were analyzed by means of a cDNA array of 18,144 non-redundant expressed sequence tags (ESTs) isolated from L. japonicus. Expression of a total of 1,076 genes was significantly accelerated during the successive stages that represent infection of Mesorhizobium loti, nodule primordium initiation, nodule organogenesis, and the onset of nitrogen fixation. These include 32 nodulin and nodulinhomolog genes as well as a number of genes involved in the catabolism of photosynthates and assimilation of fixed nitrogen that were previously known to be abundantly expressed in root nodules of many legumes. We also identified a large number of novel nodule-specific or enhanced genes, which include genes involved in many cellular processes such as membrane transport, defense responses, phytohormone synthesis and responses, signal transduction, cell wall synthesis, and transcriptional regulation. Notably, our data indicate that the gene expression profile in early steps of Rhizobium-legume interactions is considerably different from that in subsequent stages of nodule development. A number of genes involved in the defense responses to pathogens and other stresses were induced abundantly in the infection process, but their expression was suppressed during subsequent nodule formation. The results provide a comprehensive data source for investigation of molecular mechanisms underlying nodulation and symbiotic nitrogen fixation.

Genetics and functional genomics of legume nodulation

“…Interestingly, these defense-related genes were upregulated during the early stage of nodulation and then decreased in nodules [23,50,52,53], suggesting that the invading rhizobia suppress the host's defense strategies to successfully colonize roots and so form nodules. However, a large set of genes encoding nodule-specific cysteine-rich proteins, which have a putative role as antimicrobial defensins, was upregulated in M. truncatula nodules [48 ,56], but their specific metabolic function is unknown.…”

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

“…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).…”

“…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.…”

Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula

“…These transcriptomics approaches benefited from the identification of two model plants from the legume family that proved to be excellent models also for AM, Medicago truncatula (Barker et al 1990) and Lotus japonicus (Handberg and Stougaard 1992). In addition to well advanced genome sequencing projects and the existence of comprehensive mutant collections (Tadege et al 2005;Udvardi et al 2005;Young et al 2005;Sato and Tabata 2006;Town 2006), more than 330 000 ESTs were generated in the two legumes (Quackenbush et al 2001), and several expression profiling tools have been developed (Colebatch et al 2002(Colebatch et al , 2004Kouchi et al 2004;Küster et al 2004;Hohnjec et al 2005;Lohar et al 2006). …”