Michael K Udvardi

Publications of Michael K Udvardi

• MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula.

  Authors: Jerome Verdier, Jian Zhao, Ivone Torres-Jerez, Shujun Ge, Chenggang Liu, Xianzhi He, Kirankumar S Mysore, Richard A Dixon, Michael K Udvardi

  Proceedings of the National Academy of Sciences of the United States of America. 01/2012; 109(5):1766-71.

  MtPAR (Medicago truncatula proanthocyanidin regulator) is an MYB family transcription factor that functions as a key regulator of proanthocyanidin (PA) biosynthesis in the model legume MedicagoMtPAR (Medicago truncatula proanthocyanidin regulator) is an MYB family transcription factor that functions as a key regulator of proanthocyanidin (PA) biosynthesis in the model legume Medicago truncatula. MtPAR expression is confined to the seed coat, the site of PA accumulation. Loss-of-function par mutants contained substantially less PA in the seed coat than the wild type, whereas levels of anthocyanin and other specialized metabolites were normal in the mutants. In contrast, massive accumulation of PAs occurred when MtPAR was expressed ectopically in transformed hairy roots of Medicago. Transcriptome analysis of par mutants and MtPAR-expressing hairy roots, coupled with yeast one-hybrid analysis, revealed that MtPAR positively regulates genes encoding enzymes of the flavonoid-PA pathway via a probable activation of WD40-1. Expression of MtPAR in the forage legume alfalfa (Medicago sativa) resulted in detectable levels of PA in shoots, highlighting the potential of this gene for biotechnological strategies to increase PAs in forage legumes for reduction of pasture bloat in ruminant animals.

• The integral membrane protein SEN1 is required for symbiotic nitrogen fixation in Lotus japonicus nodules.

  Authors: Tsuneo Hakoyama, Kaori Niimi, Takeshi Yamamoto, Sawa Isobe, Shusei Sato, Yasukazu Nakamura, Satoshi Tabata, Hirotaka Kumagai, Yosuke Umehara, Katja Brossuleit, Thomas R Petersen, Niels Sandal, Jens Stougaard, Michael K Udvardi, Masanori Tamaoki, Masayoshi Kawaguchi, Hiroshi Kouchi, Norio Suganuma

  Plant & cell physiology. 11/2011; 53(1):225-36.

  Legume plants establish a symbiotic association with bacteria called rhizobia, resulting in the formation of nitrogen-fixing root nodules. A Lotus japonicus symbiotic mutant, sen1, forms nodules thatLegume plants establish a symbiotic association with bacteria called rhizobia, resulting in the formation of nitrogen-fixing root nodules. A Lotus japonicus symbiotic mutant, sen1, forms nodules that are infected by rhizobia but that do not fix nitrogen. Here, we report molecular identification of the causal gene, SEN1, by map-based cloning. The SEN1 gene encodes an integral membrane protein homologous to Glycine max nodulin-21, and also to CCC1, a vacuolar iron/manganese transporter of Saccharomyces cerevisiae, and VIT1, a vacuolar iron transporter of Arabidopsis thaliana. Expression of the SEN1 gene was detected exclusively in nodule-infected cells and increased during nodule development. Nif gene expression as well as the presence of nitrogenase proteins was detected in rhizobia from sen1 nodules, although the levels of expression were low compared with those from wild-type nodules. Microscopic observations revealed that symbiosome and/or bacteroid differentiation are impaired in the sen1 nodules even at a very early stage of nodule development. Phylogenetic analysis indicated that SEN1 belongs to a protein clade specific to legumes. These results indicate that SEN1 is essential for nitrogen fixation activity and symbiosome/bacteroid differentiation in legume nodules.

• The Medicago genome provides insight into the evolution of rhizobial symbioses.

  Authors: Nevin D Young, Frédéric Debellé, Giles E D Oldroyd, Rene Geurts, Steven B Cannon, Michael K Udvardi, Vagner A Benedito, Klaus F X Mayer, Jérôme Gouzy, Heiko Schoof [......] Liping Zhou, Antoine Zuber, Jean Dénarié, Richard A Dixon, Gregory D May, David C Schwartz, Jane Rogers, Francis Quétier, Christopher D Town, Bruce A Roe

  Nature. 11/2011; 480(7378):520-4.

  Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in aLegumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.

• Comparative metabolomics of drought acclimation in model and forage legumes.

  Authors: Diego H Sanchez, Franziska Schwabe, Alexander Erban, Michael K Udvardi, Joachim Kopka

  Plant, cell & environment. 09/2011; 35(1):136-49.

  Water limitation has become a major concern for agriculture. Such constraints reinforce the urgent need to understand mechanisms by which plants cope with water deprivation. We used a non-targetedWater limitation has become a major concern for agriculture. Such constraints reinforce the urgent need to understand mechanisms by which plants cope with water deprivation. We used a non-targeted metabolomic approach to explore plastic systems responses to non-lethal drought in model and forage legume species of the Lotus genus. In the model legume Lotus. japonicus, increased water stress caused gradual increases of most of the soluble small molecules profiled, reflecting a global and progressive reprogramming of metabolic pathways. The comparative metabolomic approach between Lotus species revealed conserved and unique metabolic responses to drought stress. Importantly, only few drought-responsive metabolites were conserved among all species. Thus we highlight a potential impediment to translational approaches that aim to engineer traits linked to the accumulation of compatible solutes. Finally, a broad comparison of the metabolic changes elicited by drought and salt acclimation revealed partial conservation of these metabolic stress responses within each of the Lotus species, but only few salt- and drought-responsive metabolites were shared between all. The implications of these results are discussed with regard to the current insights into legume water stress physiology.

• Nodulation enhances dark CO₂ fixation and recycling in the model legume Lotus japonicus.

  Authors: Mariangela N Fotelli, Daniela Tsikou, Anna Kolliopoulou, Georgios Aivalakis, Panagiotis Katinakis, Michael K Udvardi, Heinz Rennenberg, Emmanouil Flemetakis

  Journal of experimental botany. 02/2011; 62(8):2959-71.

  During symbiotic nitrogen fixation (SNF), the nodule becomes a strong sink for photosynthetic carbon. Here, it was studied whether nodule dark CO(2) fixation could participate in a mechanism forDuring symbiotic nitrogen fixation (SNF), the nodule becomes a strong sink for photosynthetic carbon. Here, it was studied whether nodule dark CO(2) fixation could participate in a mechanism for CO(2) recycling through C(4)-type photosynthesis. Differences in the natural δ(13)C abundance between Lotus japonicus inoculated or not with the N-fixing Mesorhizobium loti were assessed. (13)C labelling and gene expression of key enzymes of CO(2) metabolism were applied in plants inoculated with wild-type or mutant fix(-) (deficient in N fixation) strains of M. loti, and in non-inoculated plants. Compared with non-inoculated legumes, inoculated legumes had higher natural δ(13)C abundance and total C in their hypergeous organs and nodules. In stems, (13)C accumulation and expression of genes coding for enzymes of malate metabolism were greater in inoculated compared with non-inoculated plants. Malate-oxidizing activity was localized in stem xylem parenchyma, sieve tubes, and photosynthetic outer cortex parenchyma of inoculated plants. In stems of plants inoculated with fix(-) M. loti strains, (13)C accumulation remained high, while accumulation of transcripts coding for malic enzyme isoforms increased. A potential mechanism is proposed for reducing carbon losses during SNF by the direct reincorporation of CO(2) respired by nodules and the transport and metabolism of C-containing metabolites in hypergeous organs.

• Cloning and functional characterization of LjPLT4, a plasma membrane xylitol H(+)- symporter from Lotus japonicus.

  Authors: Katerina I Kalliampakou, Evangelia D Kouri, Haralabia Boleti, Ourania Pavli, Laurence Maurousset, Michael K Udvardi, Panagiotis Katinakis, Rémi Lemoine, Emmanouil Flemetakis

  Molecular membrane biology. 01/2011; 28(1):1-13.

  Polyols are compounds that play various physiological roles in plants. Here we present the identification of four cDNA clones of the model legume Lotus japonicus, encoding proteins of thePolyols are compounds that play various physiological roles in plants. Here we present the identification of four cDNA clones of the model legume Lotus japonicus, encoding proteins of the monosaccharide transporter-like (MST) superfamily that share significant homology with previously characterized polyol transporters (PLTs). One of the transporters, named LjPLT4, was characterized functionally after expression in yeast. Transport assays revealed that LjPLT4 is a xylitol-specific H(+)-symporter (K (m), 0.34 mM). In contrast to the previously characterized homologues, LjPLT4 was unable to transport other polyols, including mannitol, sorbitol, myo-inositol and galactitol, or any of the monosaccharides tested. Interestingly, some monosaccharides, including fructose and xylose, inhibited xylitol uptake, although no significant uptake of these compounds was detected in the LjPLT4 transformed yeast cells, suggesting interactions with the xylitol binding site. Subcellular localization of LjPLT4-eYFP fusions expressed in Arabidopsis leaf epidermal cells indicated that LjPLT4 is localized in the plasma membrane. Real-time RT-PCR revealed that LjPLT4 is expressed in all major plant organs, with maximum transcript accumulation in leaves correlating with maximum xylitol levels there, as determined by GC-MS. Thus, LjPLT4 is the first plasma membrane xylitol-specific H(+)-symporter to be characterized in plants.

• Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula.

  Authors: Jeremy D Murray, RajaSekhara Reddy Duvvuru Muni, Ivone Torres-Jerez, Yuhong Tang, Stacy Allen, Megan Andriankaja, Guangming Li, Ashverya Laxmi, Xiaofei Cheng, Jiangqi Wen, David Vaughan, Michael Schultze, Jongho Sun, Myriam Charpentier, Giles Oldroyd, Million Tadege, Pascal Ratet, Kirankumar S Mysore, Rujin Chen, Michael K Udvardi

  The Plant journal : for cell and molecular biology. 01/2011; 65(2):244-52.

  Intracellular invasion of root cells is required for the establishment of successful endosymbioses in legumes of both arbuscular mycorrhizal (AM) fungi and rhizobial bacteria. In both interactions aIntracellular invasion of root cells is required for the establishment of successful endosymbioses in legumes of both arbuscular mycorrhizal (AM) fungi and rhizobial bacteria. In both interactions a requirement for successful entry is the activation of a common signalling pathway that includes five genes required to generate calcium oscillations and two genes required for the perception of the calcium response. Recently, it has been discovered that in Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Here, we show by analyses of mutants that the same gene is also required for rhizobial colonization and nodulation. VPY encodes a protein featuring a Major Sperm Protein domain, typically featured on proteins involved in membrane trafficking and biogenesis, and a series of ankyrin repeats. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. Calcium spiking in root hairs in response to supplied Nod factors is intact in the vpy-1 mutant. This, and the elevation of VPY transcripts upon application of Nod factors which we show to be dependent on NFP, DMI1, and DMI3, indicates that VPY acts downstream of the common signalling pathway.

• Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis.

  Authors: Diego H Sanchez, Fernando L Pieckenstain, Francisco Escaray, Alexander Erban, Ute Kraemer, Michael K Udvardi, Joachim Kopka

  Plant, cell & environment. 01/2011; 34(4):605-17.

  The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to theThe legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl⁻ from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis.

• Characterization of two novel nodule-enhanced α-type carbonic anhydrases from Lotus japonicus.

  Authors: Daniela Tsikou, Catalina Stedel, Evangelia D Kouri, Michael K Udvardi, Trevor L Wang, Panagiotis Katinakis, Nikolaos E Labrou, Emmanouil Flemetakis

  Biochimica et biophysica acta. 01/2011; 1814(4):496-504.

  Two cDNA clones coding for α-type carbonic anhydrases (CA; EC 4.2.1.1) in the nitrogen-fixing nodules of the model legume Lotus japonicus were identified. Functionality of the full-length proteinsTwo cDNA clones coding for α-type carbonic anhydrases (CA; EC 4.2.1.1) in the nitrogen-fixing nodules of the model legume Lotus japonicus were identified. Functionality of the full-length proteins was confirmed by heterologous expression in Escherichia coli and purification of the encoded polypeptides. The developmental expression pattern of LjCAA1 and LjCAA2 revealed that both genes code for nodule enhanced carbonic anhydrase isoforms, which are induced early during nodule development. The genes were slightly to moderately down-regulated in ineffective nodules formed by mutant Mesorhizobium loti strains, indicating that these genes may also be involved in biochemical and physiological processes not directly linked to nitrogen fixation/assimilation. The spatial expression profiling revealed that both genes were expressed in nodule inner cortical cells, vascular bundles and central tissue. These results are discussed in the context of the possible roles of CA in nodule carbon dioxide (CO(2)) metabolism.

• Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics.

  Authors: Diego H Sanchez, Fernando L Pieckenstain, Jedrzey Szymanski, Alexander Erban, Mariusz Bromke, Matthew A Hannah, Ute Kraemer, Joachim Kopka, Michael K Udvardi

  PloS one. 01/2011; 6(2):e17094.

  One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding,One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl(-) correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, 'triangulation' from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species.

• Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis.

  Authors: Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D Town, Patrick X Zhao, Michael K Udvardi, Maria J Monteros

  BMC genomics. 01/2011; 12:1-11.

  Single nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolutionSingle nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM) for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L.), a species with high economic value but limited genomic resources. The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs) sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM) analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1) chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

• A remorin protein interacts with symbiotic receptors and regulates bacterial infection.

  Authors: Benoit Lefebvre, Ton Timmers, Malick Mbengue, Sandra Moreau, Christine Hervé, Katalin Tóth, Joana Bittencourt-Silvestre, Dörte Klaus, Laurent Deslandes, Laurence Godiard, Jeremy D Murray, Michael K Udvardi, Sylvain Raffaele, Sebastien Mongrand, Julie Cullimore, Pascal Gamas, Andreas Niebel, Thomas Ott

  Proceedings of the National Academy of Sciences of the United States of America. 02/2010; 107(5):2343-8.

  Remorin proteins have been hypothesized to play important roles during cellular signal transduction processes. Induction of some members of this multigene family has been reported during bioticRemorin proteins have been hypothesized to play important roles during cellular signal transduction processes. Induction of some members of this multigene family has been reported during biotic interactions. However, no roles during host-bacteria interactions have been assigned to remorin proteins until now. We used root nodule symbiosis between Medicago truncatula and Sinorhizobium meliloti to study the roles of a remorin that is specifically induced during nodulation. Here we show that this oligomeric remorin protein attaches to the host plasma membrane surrounding the bacteria and controls infection and release of rhizobia into the host cytoplasm. It interacts with the core set of symbiotic receptors that are essential for perception of bacterial signaling molecules, and thus might represent a plant-specific scaffolding protein.

• The Medicago truncatula gene expression atlas web server.

  Authors: Ji He, Vagner A Benedito, Mingyi Wang, Jeremy D Murray, Patrick X Zhao, Yuhong Tang, Michael K Udvardi

  BMC bioinformatics. 12/2009; 10(1):441.

  ABSTRACT: BACKGROUND: Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping toABSTRACT: BACKGROUND: Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publicly available microarray data using the Affymetrix GeneChip Medicago Genome Array from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. RESULTS: The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(R) Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/. CONCLUSIONS: The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.

• Genomic inventory and transcriptional analysis of Medicago truncatula transporters.

  Authors: Vagner A Benedito, Haiquan Li, Xinbin Dai, Maren Wandrey, Ji He, Rakesh Kaundal, Ivone Torres-Jerez, S Karen Gomez, Maria J Harrison, Yuhong Tang, Patrick X Zhao, Michael K Udvardi

  Plant physiology. 12/2009;

  Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, signaling, and consequently in plant growth, development, andTransporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, signaling, and consequently in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume, Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 sub-families. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule-specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least five fold during nodule development and 44 in roots during arbuscular mycorrhizal (AM) symbiosis. Amongst the nodule- and mycorrhizal-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for selection and functional characterization of legume transporters.

• TransportTP: A two-phase classification approach for membrane transporter prediction and characterization.

  Authors: Haiquan Li, Vagner A Benedito, Michael K Udvardi, Patrick Xuechun Zhao

  BMC bioinformatics. 12/2009; 10(1):418.

  ABSTRACT: BACKGROUND: Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods forABSTRACT: BACKGROUND: Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combines homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods are employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods are used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides. RESULTS: In a cross-validation using the yeast proteome for training and the proteomes of ten other organisms for testing, TransportTP achieved an equivalent recall and precision of 81.8%, based on TransportDB, a manually annotated transporter database. In an independent test using the Arabidopsis proteome for training and four recently sequenced plant proteomes for testing, it achieved a recall of 74.6% and a precision of 73.4%, according to our manual curation. CONCLUSIONS: TransportTP is the most effective tool for eukaryotic transporter characterization up to date.

• Legume transcription factor genes; what makes legumes so special?

  Authors: Marc Libault, Trupti Joshi, Vagner A Benedito, Dong Xu, Michael K Udvardi, Gary Stacey

  Plant physiology. 10/2009;

  All eukaryotic organisms have a diversity of transcription factor (TF) gene families, encoding key-proteins regulating gene expression. TF families are strongly conserved across eukaryotic organisms,All eukaryotic organisms have a diversity of transcription factor (TF) gene families, encoding key-proteins regulating gene expression. TF families are strongly conserved across eukaryotic organisms, especially plants. The specific function of each of these TF genes is of interest due to their role in controlling plant developmental processes and responses to environmental conditions, including functions of key importance to agronomic performance. In this review, we focus on the role of TF genes in legume species. The review also provides an update on the identification and categorization of TF genes in several eukaryotes, including three partially or completely sequenced legume genomes (Glycine max L. Merr., Medicago truncatula and Lotus japonicus). The role of TF genes in legumes is discussed in an evolutionary context based upon a comprehensive comparison of TF gene distribution and direct experimental data obtained for a significant number of legume TF genes.

• Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus.

  Authors: Diego H Sanchez, Jedrzej Szymanski, Alexander Erban, Michael K Udvardi, Joachim Kopka

  Plant, cell & environment. 09/2009;

  Summary The manuscript "Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus" by Sanchez DH and co-authors addressesSummary The manuscript "Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus" by Sanchez DH and co-authors addresses the experimental limitations of systems phenotyping at ionomic, metabolomic and transcriptomic levels and the resulting impact on the deductive scientific process in the context of translational genomics for crop breeding. The study formally demonstrates using legume salinity stress as an example that not only high replication within single experimental setups but more importantly independent experimentation in slightly varying environments are the strategies applicable in academia to discover functionally robust molecular and metabolic systems responses which may be successfully transferred from model species to agronomically relevant crops.

• Global Changes in the Transcript and Metabolic Profiles During Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants.

  Authors: Georgina Hernandez, Oswaldo Valdes-Lopez, Mario Ramirez, Nicolas Goffard, Georg Weiller, Rosaura Aparicio-Fabre, Sara Isabel Fuentes, Alexander Erban, Joachim Kopka, Michael K Udvardi, Carroll P Vance

  Plant physiology. 09/2009;

  Phosphorus (P) deficiency is widespread in regions where the common bean (Phaseolus vulgaris L.), the most important legume for human consumption, is produced and is perhaps the factor that mostPhosphorus (P) deficiency is widespread in regions where the common bean (Phaseolus vulgaris L.), the most important legume for human consumption, is produced and is perhaps the factor that most limits nitrogen (N) fixation. Global gene expression and metabolome approaches were used to investigate the responses of nodules from common bean plants inoculated with Rhizobium tropici CIAT899 grown under P-deficient and P-sufficient conditions. P-deficient inoculated plants showed drastic reduction in nodulation and nitrogenase activity as determined by acetylene reduction assay. Nodule transcript profiling was performed through hybridization of nylon filter arrays spotted with cDNAs, ca. 4,000 unigene set, from nodule and P-deficient root library. A total of 459 genes, representing different biological processes according to updated annotation using the UniProt Knowledgebase database, showed significant differential expression in response to P: 59% of these were induced in P-deficient nodules. The expression platform for transcription factor (TF) genes based in quantitative reverse transcriptase-polymerase chain reaction revealed that 37 TF genes were differentially expressed in P-deficient nodules, only one gene was repressed. Data from performed non-targeted metabolic profile indicated that amino acids and other N metabolites were decreased while organic and polyhydroxy acids were accumulated in P-deficient nodules. Bioinformatics analyses using MapMan and PathExpress software tools, customized to common bean, were utilized for the analysis of global changes in gene expression that affected overall metabolism. Glycolysis and glycerolipid metabolism, and starch and sucrose metabolism were identified among the pathways significantly induced or repressed in P-deficient nodules, respectively.

• Molecular and Biochemical characterization of the Parvulin-type PPIases in Lotus japonicus.

  Authors: Evangelia D Kouri, Nikolaos E Labrou, Spiros D. Garbis, Katerina I Kalliampakou, Catalina Stedel, Maria Dimou, Michael K Udvardi, Panagiotis Katinakis, Emmanouil Flemetakis

  Plant physiology. 05/2009;

  The cis/trans isomerization of the peptide bond preceding proline is an intrinsically slow process, although important in many biological processes in both prokaryotes and eukaryotes. In vivo thisThe cis/trans isomerization of the peptide bond preceding proline is an intrinsically slow process, although important in many biological processes in both prokaryotes and eukaryotes. In vivo this isomerization is catalyzed by peptidyl-prolyl cis/trans isomerases (PPIases). Here we present the molecular and biochemical characterization of parvulin-type PPIase family members of the model legume Lotus japonicus, annotated as LjPar1, LjPar2 and LjPar3. Although LjPar1 and LjPar2 were found to be homologous to PIN1-type parvulins and hPar14 from human, respectively, LjPar3 represents a novel multi-domain parvulin, apparently present only in plants, which contains an active C-terminal sulfurtransferase domain. All Lotus parvulins were heterologously expressed and purified from Escherichia coli, and purified protein verification measurements where contacted an LC-MS based proteomic method. The biochemical characterization of the recombinant Lotus parvulins revealed that they posses PPIase activity towards synthetic tetrapeptides, although they exhibited different substrate specificities depending on the amino acid N-terminal to proline. These differences were also studied in a structural context using molecular modeling of the encoded polypeptides. Real-time RT-PCR revealed that the three parvulin genes of Lotus are ubiquitously expressed in all plant organs. LjPar1 was found to be upregulated during the later stages of nodule development. Subcellular localization of LjPar-eYFP fusions expressed in Arabidopsis leaf epidermal cells revealed that LjPar1- and LjPar2-eYFP fusions were localized in the cytoplasm and in the nucleus, in contrast to LjPar3-eYFP which was clearly localized in plastids. Divergent substrate specificities, expression profiles, and sub-cellular localization indicate that plant parvulin-type PPIases are probably involved in a wide range of biochemical and physiological processes.

• AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis thaliana (L.).

  Authors: Felix Lippold, Diego H Sanchez, Magdalena Musialak, Armin Schlereth, Wolf-Ruediger Scheible, Dirk K Hincha, Michael K Udvardi

  Plant physiology. 03/2009;

  Myb transcription factors have been implicated in a wide variety of plant-specific processes, including secondary metabolism, cell-shape determination, cell differentiation, and stress responses.Myb transcription factors have been implicated in a wide variety of plant-specific processes, including secondary metabolism, cell-shape determination, cell differentiation, and stress responses. Very recently, AtMyb41 was described as a gene transcriptionally-regulated in response to salinity, desiccation, cold and ABA. The corresponding transcription factor was suggested to control stress-responses linked to cell wall modifications. In this work, we have characterized AtMyb41 further by subjecting independent AtMyb41 over-expressing lines to detailed transcriptome and metabolome analysis. Our molecular data indicate that AtMyb41 is involved in distinct cellular processes, including control of primary metabolism and negative regulation of short-term transcriptional responses to osmotic-stress.