scholarly journals Expressed Sequence Tags from Roots and Nodule Primordia of Lotus japonicus Infected with Mesorhizobium loti

2002 ◽  
Vol 15 (4) ◽  
pp. 376-379 ◽  
Author(s):  
Carsten Poulsen ◽  
Lone Pødenphant
Keyword(s):  
Expressed Sequence Tags ◽  
Messenger Rna ◽  
Root Nodules ◽  
Lotus Japonicus ◽  
Cdna Expression Library ◽  
Expression Library ◽  
Mesorhizobium Loti ◽  
Pcr Products ◽  
Plant Genes ◽  
Expressed Sequence

Messenger RNA from young Lotus japonicus roots carrying root nodule primordia appearing after inoculation with Mesorhizobium loti bacteria were used to construct a cDNA expression library. Single-pass sequencing employing colony-polymerase chain reaction (PCR) and analysis of PCR products established a total of 2,397 new expressed sequence tags (ESTs). We have putatively identified 1,236 known and 484 hypothetical proteins coded by the corresponding mRNAs. The remaining cDNAs are unknown (316) or redundant overlapping cDNAs (361). We hope that this batch of ESTs will assist in the recognition of plant genes involved during development of nitrogen-fixing root nodules.

Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1081-1088 ◽  
Author(s):  
Quang Hien Le ◽  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Caenorhabditis Elegans ◽  
Expressed Sequence Tags ◽  
Large Family ◽  
Insertion Sequences ◽  
Normal Plant ◽  
Nematode Caenorhabditis Elegans ◽  
Plant Genomes ◽  
Plant Genes ◽  
Expressed Sequence ◽  
Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

scholarly journals Analysis of expressed sequence tags derived from the endophytic fungus Neotyphodium lolii grown in vitro and in association with its host plant perennial ryegrass

2007 ◽  
Vol 13 ◽  
pp. 501-504
Author(s):  
R. Johnson ◽  
A. Khan ◽  
C. Voisey ◽  
S. Bassett ◽  
C. Gaborit ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Virulence Genes ◽  
In Planta ◽  
Suppression Subtractive Hybridisation ◽  
The Public ◽  
Neotyphodium Lolii ◽  
Subtractive Hybridisation ◽  
Plant Genes ◽  
Expressed Sequence

As a first step towards a functional genomics approach to gain a greater understanding of this important symbiosis, we have generated, sequenced and analysed two EST libraries from cultures of N. lolii and six in planta subtracted EST libraries enriched for differentially expressed genes. A total of 12871 ESTs were sequenced which, after filtering for quality, clustered into 1066 contigs and 3230 singletons to give a set of 4296 unique sequences or unigenes. BLASTX analysis revealed that 60% of fungal sequences derived from cultures were of unknown function with a sub-set of these corresponding to orphans. For the in planta-derived ESTs, most of the sequences with homologs in the public databases (98%) were of ryegrass origin. Comparisons made against fully sequenced genomes revealed that most fungal ESTs were homologous to genes present in both pathogenic and non-pathogenic ascomycete filamentous fungi, whereas the subtracted libraries comprised mostly plant genes. A range of sequences having significant homology to demonstrated pathogenicity/virulence genes in other fungal pathosystems were also identified, as well as some ESTs with proven roles in endophyte secondary metabolism. Keywords: ESTs, cDNA, Neotyphodium lolii, Lolium perenne, symbiosis, mutualism, suppression subtractive hybridisation

Development of an EST-SSR marker in Panax ginseng

2008 ◽  
Vol 5 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Yang Cheng-Jun ◽  
Wang Jun ◽  
Mu Li-Qiang ◽  
Li Shao-Chen ◽  
Liu Guan-Jun ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Expressed Sequence Tags ◽  
Genomic Dna ◽  
Ssr Marker ◽  
Panax Quinquefolius ◽  
Chain Reaction ◽  
Acanthopanax Senticosus ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Expressed Sequence

AbstractA total of 791 microsatellites (SSRs) were isolated from 7055 Panax ginseng expressed sequence tags (ESTs). According to primer design criteria, 68 primer pairs for EST-SSR were designed. Under an appropriate polymerase chain reaction (PCR) system, all EST-SSR primer pairs were screened against genomic DNA of Ji'anchangbo and Fusong'ermaya from Panax ginseng, and 43 EST-SSR primer pairs out of the above 68 resulted in PCR products. Then, all 43 pairs were detected in nine P. ginseng, two Panax quinquefolius and two Acanthopanax senticosus cultivars for polymorphisms, and 26 pairs (60.47%) were found to be polymorphic, accounting for 38.23% of the total number of designed primer pairs. These results demonstrate the possibility of developing EST-SSR markers using P. ginseng ESTs.

The elusive factor Xa receptor: failure to detect transcripts that correspond to the published sequence of EPR-1

Blood ◽  
2000 ◽  
Vol 96 (1) ◽  
pp. 145-148 ◽  
Author(s):  
Guido J. R. Zaman ◽  
Edward M. Conway
Keyword(s):  
Expressed Sequence Tags ◽  
Messenger Rna ◽  
Blot Hybridization ◽  
Factor Xa ◽  
Southern Blot Hybridization ◽  
Cellular Responses ◽  
Cellular Effects ◽  
Strong Homology ◽  
Polymerase Chain ◽  
Expressed Sequence

The coagulation protease factor Xa induces cellular responses implicated in cardiovascular and inflammatory disease. Effector-cell protease receptor 1 (EPR-1) is a functionally characterized receptor of factor Xa, and the EPR-1complementary DNA (cDNA) was published. Remarkably, the cDNA encoding an inhibitor of apoptosis, survivin, is reportedly identical to that ofEPR-1 except for a few nucleotide differences and its orientation opposite to EPR-1. To isolate the EPR-1cDNA and gene, we surveyed gene databases for expressed sequence tags (ESTs) that could be derived from EPR-1. All ESTs with strong homology to EPR-1/survivin were derived from survivinand could not encode EPR-1. By polymerase chain reaction and Southern blot hybridization, EPR-1 was not detectable in the human or murine genome, but survivin was. Our data suggest that EPR-1 is either highly cell-specific or the published EPR-1 cDNA includes sequences from clones derived from survivin messenger RNA. The means by which factor Xa mediates its cellular effects requires further evaluation.

scholarly journals Differential Effects of Combined N Sources on Early Steps of the Nod Factor–Dependent Transduction Pathway in Lotus japonicus

2007 ◽  
Vol 20 (8) ◽  
pp. 994-1003 ◽  
Author(s):  
Ani Barbulova ◽  
Alessandra Rogato ◽  
Enrica D'Apuzzo ◽  
Selim Omrane ◽  
Maurizio Chiurazzi
Keyword(s):  
Root Nodules ◽  
Lotus Japonicus ◽  
Small Scale ◽  
Nodule Formation ◽  
Inhibitory Effects ◽  
Nod Factor ◽  
Mesorhizobium Loti ◽  
N Sources ◽  
N Starvation ◽  
And Function

The development of nitrogen-fixing nodules in legumes is induced by perception of lipochitin-oligosaccharide signals secreted by a bacterial symbiont. Nitrogen (N) starvation is a prerequisite for the formation, development, and function of root nodules, and high levels of combined N in the form of nitrate or ammonium can completely abolish nodule formation. We distinguished between nitrate and ammonium inhibitory effects by identifying when and where these combined N sources interfere with the Nod-factor-induced pathway. Furthermore, we present a small-scale analysis of the expression profile, under different N conditions, of recently identified genes involved in the Nod-factor-induced pathway. In the presence of high levels of nitrate or ammonium, the NIN gene fails to be induced 24 h after the addition of Nod factor compared with plants grown under N-free conditions. This induction is restored in the hypernodulating nitrate-tolerant har1-3 mutant only in the presence of 10 and 20 mM KNO3. These results were confirmed in Lotus plants inoculated with Mesorhizobium loti. NIN plays a key role in the nodule organogenesis program and its downregulation may represent a crucial event in the nitrate-dependent pathway leading to the inhibition of nodule organogenesis.

scholarly journals Absence of Symbiotic Leghemoglobins Alters Bacteroid and Plant Cell Differentiation During Development of Lotus japonicus Root Nodules

2009 ◽  
Vol 22 (7) ◽  
pp. 800-808 ◽  
Author(s):  
Thomas Ott ◽  
John Sullivan ◽  
Euan K. James ◽  
Emmanouil Flemetakis ◽  
Catrin Günther ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Cell Differentiation ◽  
Root Nodules ◽  
Lotus Japonicus ◽  
Nodule Development ◽  
Primary And Secondary Metabolism ◽  
Bacterial Differentiation ◽  
Plant Genes ◽  
Bacterial Genes

During development of legume root nodules, rhizobia and their host plant cells undergo profound differentiation, which is underpinned by massive changes in gene expression in both symbiotic partners. Oxygen concentrations in infected and surrounding uninfected cells drop precipitously during nodule development. To assess what effects this has on plant and bacterial cell differentiation and gene expression, we used a leghemoglobin-RNA-interference (LbRNAi) line of Lotus japonicus, which is devoid of leghemoglobins and has elevated levels of free-oxygen in its nodules. Bacteroids in LbRNAi nodules showed altered ultrastructure indicating changes in bacterial differentiation. Transcript analysis of 189 plant and 192 bacterial genes uncovered many genes in both the plant and bacteria that were differentially regulated during nodulation of LbRNAi plants compared with the wild type (containing Lb and able to fix nitrogen). These included fix and nif genes of the bacteria, which are involved in microaerobic respiration and nitrogen fixation, respectively, and plant genes involved in primary and secondary metabolism. Metabolite analysis revealed decreased levels of many amino acids in nodules of LbRNAi plants, consistent with the defect in symbiotic nitrogen fixation of this line.

The elusive factor Xa receptor: failure to detect transcripts that correspond to the published sequence of EPR-1

Blood ◽  
2000 ◽  
Vol 96 (1) ◽  
pp. 145-148 ◽  
Author(s):  
Guido J. R. Zaman ◽  
Edward M. Conway
Keyword(s):  
Expressed Sequence Tags ◽  
Messenger Rna ◽  
Blot Hybridization ◽  
Factor Xa ◽  
Southern Blot Hybridization ◽  
Cellular Responses ◽  
Cellular Effects ◽  
Strong Homology ◽  
Polymerase Chain ◽  
Expressed Sequence

Abstract The coagulation protease factor Xa induces cellular responses implicated in cardiovascular and inflammatory disease. Effector-cell protease receptor 1 (EPR-1) is a functionally characterized receptor of factor Xa, and the EPR-1complementary DNA (cDNA) was published. Remarkably, the cDNA encoding an inhibitor of apoptosis, survivin, is reportedly identical to that ofEPR-1 except for a few nucleotide differences and its orientation opposite to EPR-1. To isolate the EPR-1cDNA and gene, we surveyed gene databases for expressed sequence tags (ESTs) that could be derived from EPR-1. All ESTs with strong homology to EPR-1/survivin were derived from survivinand could not encode EPR-1. By polymerase chain reaction and Southern blot hybridization, EPR-1 was not detectable in the human or murine genome, but survivin was. Our data suggest that EPR-1 is either highly cell-specific or the published EPR-1 cDNA includes sequences from clones derived from survivin messenger RNA. The means by which factor Xa mediates its cellular effects requires further evaluation.

scholarly journals Generation of 7137 Non-redundant Expressed Sequence Tags from a Legume, Lotus japonicus

DNA Research ◽  
2000 ◽  
Vol 7 (2) ◽  
pp. 127-130 ◽  
Author(s):  
E. Asamizu ◽  
Y. Nakamura ◽  
S. Sato ◽  
S. Tabata
Keyword(s):  
Expressed Sequence Tags ◽  
Lotus Japonicus ◽  
Expressed Sequence
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