Expressed sequence tags from roots and nodule primordia of Lotus japonicus infected with Mesorhizobium loti

Comparative transcriptome analysis reveals common and specific tags for root hair and crack-entry invasion in Sesbania rostrata

The tropical legume Sesbania rostrata provides its microsymbiont Azorhizobium caulinodans with versatile invasion strategies to allow nodule formation in temporarily flooded habitats. In aerated soils, the bacteria enter via the root hair curling mechanism. Submergence prevents this epidermal invasion by accumulation of inhibiting concentrations of ethylene and, under these conditions, the bacterial colonization occurs via intercellular cortical infection at lateral root bases. The transcriptome of both invasion ways was compared by cDNA-amplified fragment length polymorphism analysis. Clusters of gene tags were identified that were specific for either epidermal or cortical invasion or were shared by both. The data provide insight into mechanisms that control infection and illustrate that entry via the epidermis adds a layer of complexity to rhizobial invasion.

Desiccation-tolerance specific gene expression in leaf tissue of the resurrection plant Sporobolus stapfianus

The desiccation tolerant grass Sporobolus stapfianus Gandoger can modulate cellular processes to prevent the imposition of irreversible damage to cellular components by water deficit. The cellular processes conferring this ability are rapidly attenuated by increased water availability. This resurrection plant can quickly restore normal metabolism. Even after loss of more than 95% of its total water content, full rehydration and growth resumption can occur within 24 h. To study the molecular mechanisms of desiccation tolerance in S. stapfianus, a cDNA library constructed from dehydration-stressed leaf tissue, was differentially screened in a manner designed to identify genes with an adaptive role in desiccation tolerance. Further characterisation of four of the genes isolated revealed they are strongly up-regulated by severe dehydration stress and only in desiccation-tolerant tissue, with three of these genes not being expressed at detectable levels in hydrated or dehydrating desiccation-sensitive tissue. The nature of the putative proteins encoded by these genes are suggestive of molecular processes associated with protecting the plant against damage caused by desiccation and include a novel LEA-like protein, and a pore-like protein that may play an important role in peroxisome function during drought stress. A third gene product has similarity to a nuclear-localised protein implicated in chromatin remodelling. In addition, a UDPglucose glucosyltransferase gene has been identified that may play a role in controlling the bioactivity of plant hormones or secondary metabolites during drought stress.

Expressed sequence-tag analysis in Casuarina glauca actinorhizal nodule and root

The present study aimed to identify and assess the frequency and tissue specificity of plant genes in the actinorhizal Casuarina glauca-Frankia symbiosis through expressed sequence tag (EST) analysis. Using a custom analysis pipeline for raw sequences of C. glauca uninfected roots and nodules, we obtained an EST databank web interface. Gene expression was studied in nodules vs roots using comparative quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). From roots and nodules, 2028 ESTs were created and clustered in 242 contigs and 1429 singletons, giving a total of 1616 unique genes. Half the nodule transcripts showed no similarity to previously identified genes. Genes of primary metabolism, protein synthesis, cell division and defence were highly represented in the nodule library. Differential expression was observed between roots and nodules for several genes linked to primary metabolism and flavonoid biosynthesis. This comparative EST-based study provides the first picture of the set of genes expressed during actinorhizal symbiosis. We consider our database to be a flexible tool that can be used for the management of EST data from other actinorhizal symbioses.

Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression

We performed a comprehensive transcript analysis on the early stage of root nodulation in the model legume Lotus japonicus by serial analysis of gene expression (SAGE). SAGE libraries were made from uninfected roots and nodulating roots abundant in nodule primordia, and 85,482 and 80,233 SAGE tags were recovered, respectively. Comparison of the tag frequency identified 407 tag species that appeared in significantly greater numbers in the nodulating root than in the uninfected root, and the converse was found for 428 tag species. Gene identification of the tags was performed by matching them to L. japonicus expressed sequence tag sequences. We made several novel findings by applying SAGE to transcript analysis of legume root nodulation. A gene that showed the most significant increase in tag number upon nodulation has not been described previously. Different levels of transcription induction among leghemoglobin gene paralogs were found, indicating the effectiveness of SAGE in discriminating different gene family members. We identified genes for 44 unknown tags by means of reverse SAGE. We found 11 antisense tags that increased during nodulation, indicating that regulation of gene expression by antisense transcripts may occur in an organ-dependent manner.

Gene expression profiling of systemically wound-induced defenses in hybrid poplar

As part of an ongoing effort to identify genes involved in poplar defense responses, and to provide a resource for comparative analysis of woody and non-woody plant defense, we generated expressed sequence tags (ESTs) from a library constructed from systemically wounded leaves of hybrid poplar (Populus trichocarpa x P. deltoides). Partial sequences were obtained from the 5' ends of 928 individual cDNAs, which could be grouped into 565 non-overlapping sequences. Of these, 447 sequences were singletons, while the remainder fell into 118 clusters containing up to 17 partially overlapping ESTs. Approximately 81% of the EST sequences showed similarity to previously described sequences in public databases. Of these, the distribution of gene functions within the EST set indicated that approximately 11% of the ESTs encode proteins potentially involved in defense or secondary metabolism, while photosynthesis and primary metabolism accounted for 45% of the expressed genes. Two types of defense proteins, Kunitz trypsin inhibitors and chitinases, were found among the ten most abundant ESTs, indicating the significant impact of wounding on the leaf transcriptome and suggesting that these functions are important for hybrid poplar defense. In the course of this work, three new wound-inducible Kunitz trypsin inhibitor-like genes and two new chitinase-like genes were characterized. A suite of other systemically wound-induced genes were identified using northern and macroarray analysis, indicating diversity and multiplicity in the induced defense response. Overall, we demonstrate that defense-related genes of hybrid poplar have a variety of functions, and show remarkably diverse expression patterns upon wounding.

Computational identification and characterization of novel genes from legumes

The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.

Analysis of expressed sequence tags from roots of resistant soybean infected by the soybean cyst nematode

The soybean cyst nematode (SCN) Heterodera glycines is the most devastating pest of soybean in the U.S.A. The resistance response elicited by SCN in soybean is complex, and genes involved in the response to a large extent are unknown and not well characterized. We constructed cDNA libraries made from mRNA extracted from roots of the resistant soybean Glycine max L. Merr. 'Peking' at 12 h, 2 to 4 days, and 6 to 8 days post inoculation with the soybean cyst nematode, population NL1-RHp, similar to race 3. Expressed sequence tag analysis of the libraries provides rapid discovery of genes involved in the response of soybean to the nematode. A total of 3454 cDNA clones were examined from the three libraries, of which 25 cDNAs were derived from nematode RNA. The levels of certain stress-induced genes such as SAM22 and glutathione S-transferase (GST8) were elevated in the SCN-infected roots relative to uninoculated roots. Early defense response genes, particularly ascorbate peroxidase and lipoxygenase, were abundant in the 12-h library. By 6-8 days, the expression of most of those genes was not as abundant, whereas genes coding for unknown proteins and stress-induced proteins continued to be highly expressed. These ESTs and associated information will be useful to scientists examining gene and protein interactions between nematodes and plants.

Organogenesis of legume root nodules

The N(2)-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.

Characterization and expression analysis of genes encoding phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxylase kinase of Lotus japonicus, a model legume

Phosphoenolpyruvate carboxylases (PEPCs), one form of which in each legume species plays a central role in the carbon metabolism in symbiotic root nodules, are activated through phosphorylation of a conserved residue by a specific protein kinase (PEPC-PK). We characterized the cDNAs for two PEPC isoforms of Lotus japonicus, an amide-translocating legume that forms determinate nodules. One gene encodes a nodule-enhanced form, which is more closely related to the PEPCs in amide-type indeterminate nodules than those in ureide-type determinate nodules. The other gene is expressed in shoots and roots at a low level. Both forms have the putative phosphorylation site, Ser11. We also isolated a cDNA and the corresponding genomic DNA for PEPC-PK of L. japonicus. The recombinant PEPC-PK protein expressed in Escherichia coli phosphorylated recombinant maize C4-form PEPC efficiently in vitro. The level of mRNA for PEPC-PK was high in root nodules, and those in shoots and roots were also significant. In situ hybridization revealed that the expression patterns of the transcripts for PEPC and PEPC-PK were similar in mature root nodules, but were different in emerging nodules. When L. japonicus seedlings were subjected to prolonged darkness and subsequent illumination, the activity of PEPC-PK and the mRNA levels of both PEPC and PEPC-PK in nodules decreased and then recovered, suggesting that they are regulated according to the amounts of photosynthates transported from shoots.

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis

We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by 'electronic northern' representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.