scholarly journals Potato Homologs of Arabidopsis thaliana Genes Functional in Defense Signaling—Identification, Genetic Mapping, and Molecular Cloning

2005 ◽  
Vol 18 (10) ◽  
pp. 1107-1119 ◽  
Author(s):  
Karolina M. Pajerowska ◽  
Jane E. Parker ◽  
Christiane Gebhardt
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Expressed Sequence Tag ◽  
Quantitative Resistance ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Signaling Cascades ◽  
Defense Signaling ◽  
Expressed Sequence

Defense against pests and pathogens is a fundamental process controlled by similar molecular mechanisms in all flowering plants. Using Arabidopsis thaliana as a model, steps of the signal transduction pathways that link pathogen recognition to defense activation have been identified and corresponding genes have been characterized. Defense signaling (DS) genes are functional candidates for controlling natural quantitative variation of resistance to plant pathogens. Nineteen Arabidopsis genes operating in defense signaling cascades were selected. Solanaceae EST (expressed sequence tag) databases were employed to identify the closest homologs of potato (Solanum tuberosum). Sixteen novel DS potato homologs were positioned on the molecular maps. Five DS homologs mapped close to known quantitative resistance loci (QRL) against the oomycete Phytophthora infestans causing late blight and the bacterium Erwinia carotovora subsp. atroseptica causing blackleg of stems and tuber soft rot. The five genes are positional candidates for QRL and are highly sequence related to Arabidopsis genes AtSGT1b, AtPAD4, and AtAOS. Full-length complementary DNA and genomic sequences were obtained for potato genes StSGT1, StPAD4, and StEDS1, the latter being a putative interactor of StPAD4. Our results form the basis for further studies on the contributions of these candidate genes to natural variation of potato disease resistance.

A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart

2004 ◽  
Vol 17 (2) ◽  
pp. 245-252 ◽  
Author(s):  
Jennifer J.S. Laffin ◽  
Todd E. Scheetz ◽  
Maria de Fatima Bonaldo ◽  
Rebecca S. Reiter ◽  
Shereen Chang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expressed Sequence Tag ◽  
Heart Defects ◽  
The United States ◽  
Cdna Libraries ◽  
Tissue Samples ◽  
Rat Hearts ◽  
Subtracted Cdna Libraries ◽  
Gene Expression Studies ◽  
Expressed Sequence

Congenital heart defects affect ∼1,000,000 people in the United States, with 40,000 new births contributing to that number every year. A large percentage of these defects can be attributed to septal defects. We assembled a nonredundant collection of over 12,000 expressed sequence tags (ESTs) from a total of 30,000 ESTs, with the ultimate goal of identifying spatially and/or temporally regulated genes during heart septation. These ESTs were compiled from nonnormalized, normalized, and serially subtracted cDNA libraries derived from two sets of tissue samples. The first includes microdissected rat hearts from embryonic (E) days E13, E15, and E16.5–E18.5 and adult heart. The second includes hearts from embryonic days E17, E19, and E21 and postnatal (P) days P1, P12, P74, and P200. Over 6,000 novel ESTs were identified in the libraries derived from these two sets of tissues, all of which have been contributed to the NCBI rat UniGene collection. It is anticipated that such EST and cDNA clone resources will prove invaluable to gene expression studies aimed at the understanding of the molecular mechanisms underlying heart septation defects.

scholarly journals Mapping expressed sequence tag sites on yeast artificial chromosome clones of Arabidopsis thaliana DNA.

1997 ◽  
Vol 7 (1) ◽  
pp. 1-9 ◽  
Author(s):  
F D Agyare ◽  
D A Lashkari ◽  
A Lagos ◽  
A F Namath ◽  
G Lagos ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Yeast Artificial Chromosome ◽  
Expressed Sequence Tag ◽  
Artificial Chromosome ◽  
Expressed Sequence

Construction of cDNA library from Prunus campanulata leaves and preliminary expressed sequence tag (EST) analysis during cold stress

Biologia ◽  
2015 ◽  
Vol 70 (8) ◽  
Author(s):  
Ying-Hui Zhang ◽  
Jun-Dong Rong ◽  
Li-Guang Chen ◽  
Ling-Yan Chen ◽  
Tian-You He ◽  
...  
Keyword(s):  
Gene Expression ◽  
Low Temperature ◽  
Cold Stress ◽  
Cdna Library ◽  
Molecular Mechanisms ◽  
Expressed Sequence Tag ◽  
Go Annotation ◽  
Est Analysis ◽  
Young Leaves ◽  
Expressed Sequence

AbstractThe molecular mechanisms underlying cold-resistance in Prunus campanulata Maxim. (P. campanulata) are not fully understood. This study aimed to establish a full-length library and analyze expressed sequence tags (ESTs) to provide tools to investigate the mechanisms of P. campanulata growth at low temperatures. Based on the switching mechanism at 5’end of RNA transcript technology, a full-1ength cDNA library was generated from young leaves of P. campanulata after 72 h treatment at 1◦C, and a preliminary EST analysis was carried out. Quantitative reverse transcription polymerase chain reaction was used to assess the expression of selected cold-related genes. The cDNA library titer was 1.2 × 106 cfu/mL−1, with a recombinant rate of 96%. The average size of inserted cDNA fragments was 1.3 Kb. EST data revealed the existence of 834 clones representing a total of 667 unigenes, including 574 singletons and 93 contigs. Blast analysis identified 475 unigenes with known and putative functions. Based on similarity search and GO annotation, 84 unigenes were associated with “response to stimuli”, suggesting that cold stress induced significant alterations in gene expression in P. campanulata cultivated at 1◦C for 72 h. Interestingly, DRP, MYB, HSP, GPX and GA20-ox gene expression was significantly up-regulated in plants cultivated at low temperature, while transcript levels of TIL, CDPK were decreased. P. campanulata cultivating at low temperature express genes associated with “response to stimuli”, and in particular DRP, MYB, HSP, GPX and GA20-ox gene are up-regulated while TIL, CDPK are downregulated in response to low temperature-stress

scholarly journals Use of a Pooled Transposon Mutation Grid to Demonstrate Roles in Disease Development for Erwinia carotovora subsp. atroseptica Putative Type III Secreted Effector (DspE/A) and Helper (HrpN) Proteins

2004 ◽  
Vol 17 (9) ◽  
pp. 943-950 ◽  
Author(s):  
Maria C. Holeva ◽  
Kenneth S. Bell ◽  
Lizbeth J. Hyman ◽  
Anna O. Avrova ◽  
Stephen C. Whisson ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Plant Pathogens ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Disease Development ◽  
Type Iii ◽  
Novel Approach ◽  
Related Plant ◽  
Polymerase Chain ◽  
Soft Rot Erwinia

Soft rot Erwinia spp., like other closely related plant pathogens, possess a type III secretion system (TTSS) (encoded by the hrp gene cluster) implicated in disease development. We report the sequence of the entire hrp gene cluster and adjacent dsp genes in Erwinia carotovora subsp. atroseptica SCRI1039. The cluster is similar in content and structural organization to that in E. amylovora. However, eight putative genes of unknown function located within the E. carotovora subsp. atroseptica cluster do not have homologues in the E. amylovora cluster. An arrayed set of Tn5 insertional mutants (mutation grid) was constructed and pooled to allow rapid isolation of mutants for any given gene by polymerase chain reaction screening. This novel approach was used to obtain mutations in two structural genes (hrcC and hrcV), the effector gene dspE/A, and the helper gene hrpN. An improved pathogenicity assay revealed that these mutations led to significantly reduced virulence, showing that both the putative E. carotovora subsp. atroseptica TTSS-delivered effector and helper proteins are required for potato infection.

scholarly journals Erwinia carotovora subsp. carotovora and Erwinia-Derived Elicitors HrpN and PehA Trigger Distinct but Interacting Defense Responses and Cell Death in Arabidopsis

2003 ◽  
Vol 16 (3) ◽  
pp. 179-187 ◽  
Author(s):  
Tarja Kariola ◽  
Tiina A. Palomäki ◽  
Günter Brader ◽  
E. Tapio Palva
Keyword(s):  
Erwinia Carotovora ◽  
Soft Rot ◽  
Defense Responses ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Plant Responses ◽  
Virulence Determinants ◽  
Lesion Formation ◽  
Defense Gene Expression ◽  
Defense Signaling

We have used an hrp-positive strain of the soft rot pathogen Erwinia carotovora subsp. carotovora to elucidate plant responses to this bacterial necrotroph. Purified virulence determinants, harpin (HrpN) and polygalacturonase (PehA), were used as tools to facilitate this analysis. We show that HrpN elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis. Establishment of resistance is accompanied by the expression of salicylic acid (SA)-dependent, but also jasmonate/ethylene (JA/ET)-dependent, marker genes PR1 and PDF1.2, respectively, suggesting that both SA-dependent and JA/ET-dependent defense pathways are activated. Use of pathway-specific mutants and transgenic NahG plants show that both pathways are required for the induction of resistance. Arabidopsis plants treated simultaneously with both elictors PehA, known to trigger only JA/ET-dependent defense signaling, and HrpN react with accelerated and enhanced induction of the marker genes PR1 and PDF1.2 both locally and systemically. This mutual amplification of defense gene expression involves both SA-dependent and JA/ET-dependent defense signaling. The two elicitors produced by E. carotovora subsp. carotovora also cooperate in triggering increased production of superoxide and lesion formation.

scholarly journals Type III Secretion Contributes to the Pathogenesis of the Soft-Rot Pathogen Erwinia carotovora: Partial Characterization of the hrp Gene Cluster

2001 ◽  
Vol 14 (8) ◽  
pp. 962-968 ◽  
Author(s):  
A. Rantakari ◽  
O. Virtaharju ◽  
S. Vähämiko ◽  
S. Taira ◽  
E. T. Palva ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Iii Secretion ◽  
Plant Pathogens ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Hypersensitive Reaction ◽  
Virulence Determinants ◽  
Type Iii ◽  
Hrp Genes ◽  
Soft Rot Erwinia

The virulence of soft-rot Erwinia species is dependent mainly upon secreted enzymes such as pectinases, pectin lyases, and proteases that cause maceration of plant tissue. Some soft-rot Erwinia spp. also harbor genes homologous to the hypersensitive reaction and pathogenesis (hrp) gene cluster, encoding components of the type III secretion system. The hrp genes are essential virulence determinants for numerous nonmacerating gram-negative plant pathogens but their role in the virulence of soft-rot Erwinia spp. is not clear. We isolated and characterized 11 hrp genes of Erwinia carotovora subsp. carotovora. Three putative σL-dependent Hrp box promoter sequences were found. The genes were expressed when the bacteria were grown in Hrp-inducing medium. The operon structure of the hrp genes was determined by mRNA hybridization, and the results were in accordance with the location of the Hrp boxes. An E. carotovora strain with mutated hrcC, an essential hrp gene, was constructed. The hrcC¯ strain was able to multiply and cause disease in Arabidopsis, but the population kinetics were altered so that growth was delayed during the early stages of infection.

scholarly journals Arabidopsis thaliana Cells: A Model to Evaluate the Virulence of Pectobacterium carotovorum

2010 ◽  
Vol 23 (2) ◽  
pp. 139-143 ◽  
Author(s):  
Meriam Terta ◽  
Mohamed Kettani-Halabi ◽  
Khadija Ibenyassine ◽  
Daniel Tran ◽  
Patrice Meimoun ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Death ◽  
Plant Cell ◽  
Plant Pathogens ◽  
Plant Cell Wall ◽  
Pectate Lyase ◽  
Soft Rot ◽  
Pectobacterium Carotovorum ◽  
Cell Wall Degrading Enzymes ◽  
Suspension Cells

Pectobacterium carotovorum are economically important plant pathogens that cause plant soft rot. These enterobacteria display high diversity world-wide. Their pathogenesis depends on production and secretion of virulence factors such as plant cell wall–degrading enzymes, type III effectors, a necrosis-inducing protein, and a secreted virulence factor from Xanthomonas spp., which are tightly regulated by quorum sensing. Pectobacterium carotovorum also present pathogen-associated molecular patterns that could participate in their pathogenicity. In this study, by using suspension cells of Arabidopsis thaliana, we correlate plant cell death and pectate lyase activities during coinfection with different P. carotovorum strains. When comparing soft rot symptoms induced on potato slices with pectate lyase activities and plant cell death observed during coculture with Arabidopsis thaliana cells, the order of strain virulence was found to be the same. Therefore, Arabidopsis thaliana cells could be an alternative tool to evaluate rapidly and efficiently the virulence of different P. carotovorum strains.

scholarly journals Two E3 ligases antagonistically regulate the UV-B response inArabidopsis

2019 ◽  
Vol 116 (10) ◽  
pp. 4722-4731 ◽  
Author(s):  
Hui Ren ◽  
Jiupan Han ◽  
Panyu Yang ◽  
Weiwei Mao ◽  
Xin Liu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Molecular Mechanisms ◽  
Signaling Cascades ◽  
Light Signaling ◽  
Adaptive Responses ◽  
E3 Ligases ◽  
Light Levels ◽  
Environmental Light ◽  
Inducible Protein

Photomorphogenesis is a pivotal developmental strategy used by plants to respond to environmental light levels. During emergence from the soil and the establishment of photomorphogenesis, seedlings encounter increasing levels of UV-B irradiation and develop adaptive responses accordingly. However, the molecular mechanisms that orchestrate UV-B signaling cascades remain elusive. Here, we provide biochemical and genetic evidence that the prolonged signaling circuits of UV-B–induced photomorphogenesis involve two sets of E3 ligases and a transcription factor inArabidopsis thaliana. The UV-B–inducible protein RUP1/RUP2 associates with the CUL4-DDB1 scaffold to form an E3 ligase, which represses photomorphogenesis by mediating the degradation of HY5, the hub transcription factor in the light signaling pathway. Conversely, COP1 directly targets RUP1/RUP2 for ubiquitination and degradation, leading to balanced RUP1/RUP2 accumulation, alleviation of the COP1–HY5 interaction, and stabilization of HY5 protein. Therefore, our study reveals that these two E3-substrate modules, CUL4-DDB1-RUP1/RUP2-HY5 and COP1-RUP1/RUP2, constitute the repression and derepression machinery by which plants respond to prolonged UV-B irradiation in photomorphogenic development.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1114-1121 ◽  
Author(s):  
Shu-Mei Jiang ◽  
Long Zhang ◽  
Jun Hu ◽  
Rui Shi ◽  
Guang-He Zhou ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Expressed Sequence Tag ◽  
Barley Yellow Dwarf Virus ◽  
Differentially Expressed ◽  
Addition Line ◽  
Alien Chromosome ◽  
Thinopyrum Intermedium ◽  
Barley Yellow Dwarf ◽  
Yellow Dwarf Virus ◽  
Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

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