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The Arabidopsis Stress Responsive Gene Database  [PDF]
Subhomoi Borkotoky,Vijayakumar Saravanan,Amit Jaiswal,Bipul Das,Suresh Selvaraj,Ayaluru Murali,P. T. V. Lakshmi
International Journal of Plant Genomics , 2013, DOI: 10.1155/2013/949564
Abstract: Plants in nature may face a wide range of favorable or unfavorable biotic and abiotic factors during their life cycle. Any of these factors may cause stress in plants; therefore, they have to be more adaptable to stressful environments and must acquire greater response to different stresses. The objective of this study is to retrieve and arrange data from the literature in a standardized electronic format for the development of information resources on potential stress responsive genes in Arabidopsis thaliana. This provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of various stress responsive genes in Arabidopsis thaliana. The database is based exclusively on published stress tolerance genes associated with plants. 1. Introduction Stress response is the general term for defining the interaction between plants and the extreme environmental conditions. The study of mechanisms of adaptation to stressful and extreme environments provides the basis for addressing environmental, toxicological, and physiological problems [1]. Changes in the expression of individual genes and proteins induced by stress have been monitored under different conditions. As of the year 2000, the sequence of the Arabidopsis thaliana genome is nearly completed, and soon a catalog of plant gene expression exceeding a million transcripts will be available [2]. Here, we have listed the stress responsive genes for Arabidopsis thaliana (thale cress), a member of the mustard family, that has become a widely used model for the study of plant biology because of its small size, short generation time, facile genetics, and ease of transformation [3]. There are few databases that have been designed for stress responsive genes in plants. Plant Stress Gene Database [4] include 259 stress-related genes of 11 species along with all the available information about the individual genes. While it contains only 33 genes from Arabidopsis thaliana, our database contains 637 gene entries related to stress response in Arabidopsis thaliana. Another example—STIFDB—Arabidopsis Stress Responsive Transcription Factor Database [5], is a comprehensive collection of abiotic stress responsive genes in Arabidopsis thaliana, with options to identify probable transcription factor binding sites in their promoters, which is limited to only abiotic stress. Apart from these, we have The Arabidopsis Information Resource (TAIR) [6, 7], genetic and molecular biology data for the model higher plant Arabidopsis thaliana, which is more widespread to different aspects
T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics
Radhamony,Resmi Nath; Mohan Prasad,Anand; Srinivasan,Ramamurthy;
Electronic Journal of Biotechnology , 2005,
Abstract: with the availability of complete genome sequences of several organisms, the focus has shifted from structural genomics to functional genomics, specifically in plants where the complete genomic sequences are becoming available i.e., arabidopsis and rice. agrobacterium mediated transformation which is exploited for transgenic technology is also being used as an effective mutagen and as a tool for functional genomics in higher plants. besides the fact that the insertion of t-dna element into a gene can lead to loss or gain of function, ingenious use of a variety of vectors have led to the identification of genes and regulatory elements in arabidopsis. in this review, we highlight the progress made in the field of functional genomics of arabidopsis using t-dna tagging. since this strategy has been very successfully employed in arabidopsis and is now being extended to other plant species, we discuss the various vectors and experimental approaches employed to tag, identify and clone genes and promoter elements in arabidopsis using t-dna as a tool.
How effective is T-DNA insertional mutagenesis in Arabidopsis?  [cached]
Yi Hong Wang
Journal of Biochemical Technology , 2008,
Abstract: To evaluate the effectiveness of T-DNA insertion in knocking out agene, 1084 published Arabidopsis thaliana insertion mutantsrepresenting 755 genes in 648 publications were reviewed. Insertionin the protein-coding region of a gene generates a knockout at least90% of the time or 25% of the time if it is before the start codonwhich also produces a knockdown 67% of the time. Insertion afterthe stop codon had no effect on transcription of the upstream gene17% of the time compared to 8% in insertion before the start codon.T-DNA insertion can also cause deletion and translocation.
Genetic and Phenotypic Analyses of a Papaver somniferum T-DNA Insertional Mutant with Altered Alkaloid Composition  [PDF]
Noriaki Kawano,Fumiyuki Kiuchi,Nobuo Kawahara,Kayo Yoshimatsu
Pharmaceuticals , 2012, DOI: 10.3390/ph5020133
Abstract: The in vitro shoot culture of a T-DNA insertional mutant of Papaver somniferum L. established by the infection of Agrobacterium rhizogenes MAFF03-01724 accumulated thebaine instead of morphine as a major opium alkaloid. To develop a non-narcotic opium poppy and to gain insight into its genetic background, we have transplanted this mutant to soil, and analyzed its alkaloid content along with the manner of inheritance of T-DNA insertion loci among its selfed progenies. In the transplanted T 0 primary mutant, the opium (latex) was found to be rich in thebaine (16.3% of dried opium) by HPLC analysis. The analyses on T-DNA insertion loci by inverse PCR, adaptor-ligation PCR, and quantitative real-time PCR revealed that as many as 18 copies of T-DNAs were integrated into a poppy genome in a highly complicated manner. The number of copies of T-DNAs was decreased to seven in the selected T 3 progenies, in which the average thebaine content was 2.4-fold that of the wild type plant. This may indicate that the high thebaine phenotype was increasingly stabilized as the number of T-DNA copies was decreased. In addition, by reverse transcription PCR analysis on selected morphine biosynthetic genes, the expression of codeine 6- O-demethylase was clearly shown to be diminished in the T 0 in vitro shoot culture, which can be considered as one of the key factors of altered alkaloid composition.
Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection  [PDF]
Jennifer N. Bragg, Jiajie Wu, Sean P. Gordon, Mara E. Guttman, Roger Thilmony, Gerard R. Lazo, Yong Q. Gu, John P. Vogel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041916
Abstract: The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.
STIFDB—Arabidopsis Stress Responsive Transcription Factor DataBase  [PDF]
K. Shameer,S. Ambika,Susan Mary Varghese,N. Karaba,M. Udayakumar,R. Sowdhamini
International Journal of Plant Genomics , 2009, DOI: 10.1155/2009/583429
Abstract: Elucidating the key players of molecular mechanism that mediate the complex stress-responses in plants system is an important step to develop improved variety of stress tolerant crops. Understanding the effects of different types of biotic and abiotic stress is a rapidly emerging domain in the area of plant research to develop better, stress tolerant plants. Information about the transcription factors, transcription factor binding sites, function annotation of proteins coded by genes expressed during abiotic stress (for example: drought, cold, salinity, excess light, abscisic acid, and oxidative stress) response will provide better understanding of this phenomenon. STIFDB is a database of abiotic stress responsive genes and their predicted abiotic transcription factor binding sites in Arabidopsis thaliana. We integrated 2269 genes upregulated in different stress related microarray experiments and surveyed their 1000 bp and 100 bp upstream regions and 5UTR regions using the STIF algorithm and identified putative abiotic stress responsive transcription factor binding sites, which are compiled in the STIFDB database. STIFDB provides extensive information about various stress responsive genes and stress inducible transcription factors of Arabidopsis thaliana. STIFDB will be a useful resource for researchers to understand the abiotic stress regulome and transcriptome of this important model plant system.
Increased sensitivity to drought stress in atlon4 Arabidopsis mutant
XiaoYi Li,Ying Mu,XuWu Sun,LiXin Zhang
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-010-4166-4
Abstract: The ATP-dependent serine protease Lon belongs to the AAA+ superfamily, which is widely distributed in bacteria, archaea, and eukaryotic cells. Lon participates in the regulation of numerous physiological processes and gene expression via degrading various unstable and non-native regulators. In this study, we showed that the Arabidopsis atlon4 mutant is more sensitive to drought stress than wild-type plants. Compared with wild-type plants, atlon4 mutant plants showed increased water loss, decreased water use efficiency, and impaired stomatal closure in drought stress conditions.
Carbon Dynamics, Development and Stress Responses in Arabidopsis: Involvement of the APL4 Subunit of ADP-Glucose Pyrophosphorylase (Starch Synthesis)  [PDF]
Cécile Sulmon, Gwenola Gouesbet, Fanny Ramel, Francisco Cabello-Hurtado, Christophe Penno, Nicole Bechtold, Ivan Couée, Abdelhak El Amrani
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026855
Abstract: An Arabidopsis thaliana T-DNA insertional mutant was identified and characterized for enhanced tolerance to the singlet-oxygen-generating herbicide atrazine in comparison to wild-type. This enhanced atrazine tolerance mutant was shown to be affected in the promoter structure and in the regulation of expression of the APL4 isoform of ADP-glucose pyrophosphorylase, a key enzyme of the starch biosynthesis pathway, thus resulting in decrease of APL4 mRNA levels. The impact of this regulatory mutation was confirmed by the analysis of an independent T-DNA insertional mutant also affected in the promoter of the APL4 gene. The resulting tissue-specific modifications of carbon partitioning in plantlets and the effects on plantlet growth and stress tolerance point out to specific and non-redundant roles of APL4 in root carbon dynamics, shoot-root relationships and sink regulations of photosynthesis. Given the effects of exogenous sugar treatments and of endogenous sugar levels on atrazine tolerance in wild-type Arabidopsis plantlets, atrazine tolerance of this apl4 mutant is discussed in terms of perception of carbon status and of investment of sugar allocation in xenobiotic and oxidative stress responses.
Isolation and Analysis of Oxalic Acid Insensitive Mutant of Arabidopsis thaliana

Xiaoting Chen,Fangfang Chen,Liqun Chen,Lin Zheng,Guodong Lu,Zonghua Wang,

生物工程学报 , 2008,
Abstract: Oxalic acid (OA) is inhibitory to many fungal plant pathogens. To further characterize the molecular mechanism of OA involved in fungal pathogenesis, OA insensitive mutants were screened from a chemical inducible Arabidopsis mutant library (about 6000 lines) using MS medium (calcium free) containing 1.2 mmol/L OA and 10 micromol/L estradiol. Harvested putative mutants were collected separately. Individual lines of mutants were screened again on modified MS medium containing OA. Mutants D33, D74, D154, D282 and D630 with enhanced OA resistance were obtained. The T-DNA flanking sequences were amplified by TAIL-PCR. The sequences were blasted against TAIR database. The result indicated that the T-DNA of mutant D33 was inserted between At2g39720 (zinc finger) and At2g39730 (Rubisco activase), and the T-DNA junctions of the other four mutants were the same, all inserted in the same site of the first intron of At5g10450 (14-3-3 protein GF14 lambda).
Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana  [PDF]
Danforth Weems,Neil Miller,Margarita Garcia-Hernandez,Eva Huala,Seung Y. Rhee
Comparative and Functional Genomics , 2004, DOI: 10.1002/cfg.408
Abstract: The Arabidopsis Information Resource (TAIR) is a web-based community database for the model plant Arabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.
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