vol1no1_5 by Computing.Journal


									                                          VOL. 1, NO. 1, November 2011                                             ISSN XXXX-XXXX
                                           ARPN Journal of Science and Technology
                                               ©2011-2012 ARPN Journals. All rights reserved.


    Plant Stress Gene Database: A Collection of Plant Genes Responding to
                              Stress Condition
                                   Ratna Prabha1,2, Indira Ghosh3 , Dhananjaya P. Singh 4

    1                                                      3                                      4
       Project Trainee, School of Information               Dean, Professor                         Senior Scientist,
    Technology,                                            School of Information Technology,      National Bureau of Agriculturally
    JNU, New Delhi- 110067, India.                         JNU, New Delhi- 110067, India          Important Microorganisms,
    Email: ratna.bioinfo@gmail.com                                                                Kushmaur,
      Current Address: Senior Research Fellow,                                                    Mau Nath Bhanjan -275101, U. P.,
    National Bureau of Agriculturally Important                                                   India
    Mau Nath Bhanjan -275101, U. P., India

Plants are exposed to variety of stress factors (biotic and abiotic) in both natural and agricultural conditions, which have a
serious impact on plant development and growth. Plants adapt to these stresses through a series of events which occurs at
every level of plant organization i.e. cellular, biochemical and molecular level. This complex response requires an
extensive molecular regulation of gene expression. Understanding the mechanisms by which plants perceive environmental
signals and transmit the signals to cellular machinery to activate adaptive responses is of fundamental importance to
biology and has been intensively investigated in recent years. We developed a database namely, Plant Stress Gene
Database which provides information about the genes involved in stress conditions in plants. A total of 259 genes from 11
plant species (Arabidopsis thaliana, Arachis hypogaea, Glycine max, Hordeum vulgare, Oryza sativa, Pennisetum,
Phaseolus vulgaris, Saccharum officinarum, Solanum lycopersicum, Triticum aestivum and Zea mays) are available in it.
This database attempts to provide all the available information about these genes along with their ortholog and paralog.
Database is publicly accessible at http://ccbb.jnu.ac.in/stressgenes/frontpage.html.

Keywords: Plant stress gene database, Plant stress, Abiotic stress, Stress database, Stress gene database, Plant stress gene.

1. INTRODUCTION                                                                Presently only one database [3] is available on plant
                                                                          stress i.e. Plant stress-responsive gene catalogue [4]. This
     Defining the term stress in plant physiology is very                 database is a compendium of protein families,
critical primarily because of the complex interaction                     phylogenetic trees, multiple sequence alignments (MSA)
between plants and the environment. Stress is used in a                   and associated experimental evidence. Owing to the
very general sense to denote an adverse environmental                     importance of plant genes which are involved in different
condition that inhibits plants from normal functioning.                   types of stress conditions, we have designed a specific
Environmental stresses represent the most limiting factors                database “Plant Stress Gene Database” (Fig.1) that focus
for agricultural productivity. Apart from biotic stress                   on plant genes involved in stress conditions rather than
caused by plant pathogens, there are a number of abiotic                  protein                                             families
stresses such as extremes in temperature, drought, salinity,              (http://ccbb.jnu.ac.in/stressgenes/frontpage.html).
heavy metals and radiation and all have detrimental effects
on plant growth and yield [1].                                            2. MATERIALS AND METHODS
     For survival under such conditions, plants have
evolved intricate mechanisms to perceive external signals,                     Literature search was carried out using combinations
allowing optimal response to environmental conditions.                    of keywords and limiting the search to plant species to
Many phytohormones such as salicylic acid (SA),                           identify stress-related genes. Genes and additional
jasmonic acid (JA), ethylene (ET), and abscisic acid                      information was retrieved from different databases, such
(ABA) regulate the protective responses of plants against                 NCBI, DDBJ, EMBL etc. All the genes were grouped
both biotic and abiotic stresses via synergistic and                      according to plant species to which they belong.
antagonistic actions referred to as signaling crosstalk.                       MySQL, a relational database management system
Moreover, the generation of reactive oxygen species                       (RDBMS) which has more than 11 million installations is
(ROS) has been proposed as a key process shared between                   used for data storage. Web interfaces for database and the
biotic and abiotic stress responses. Biotic and abiotic                   browse result pages were developed using HTML and
stresses regulate the expression of different but                         PHP scripts respectively. Data Collection and
overlapping suites of genes [2].                                          organizational structure of database is shown in Fig 2.

VOL. 1, NO. 1, November 2011                          ISSN XXXX-XXXX
 ARPN Journal of Science and Technology
     ©2011-2012 ARPN Journals. All rights reserved.


Fig. 1: Home page of Plant Stress Gene Database

                                       VOL. 1, NO. 1, November 2011                                            ISSN XXXX-XXXX
                                        ARPN Journal of Science and Technology
                                            ©2011-2012 ARPN Journals. All rights reserved.


                                         Fig. 2: Organizational structure of Database

          Tabular style was used for information                          which provide link to other important databases,
representation. At the home page, a brief introduction                    basically those from which information was extracted
about database is given along with the name of species                    during compilation of this database.
included in database. For each plant species, a separate
web page was created which includes information of all                    3. RESULTS AND DISCUSSION
genes of that species as a spreadsheet and each row
represents one gene.                                                                A database named Plant Stress Gene Database
          Information for any gene in database is divided                 (online                     available                  at
in three sections:                                                        http://ccbb.jnu.ac.in/stressgenes/frontpage.html) of 259
          (i) Information about Gene; its accession                       genes from 11 plant species (Arabidopsis thaliana,
number, other names for gene (if available), coding                       Arachis hypogaea, Glycine max, Hordeum vulgare,
property and link to its nucleotide sequence.                             Oryza sativa, Pennisetum, Phaseolus vulgaris,
          (ii) If gene is protein coding, then protein name,              Saccharum officinarum, Solanum lycopersicum,
accession number, external link to sequence, information                  Triticum aestivum and Zea mays) which were involved
about their ortholog and paralogs.                                        in stress condition, was developed using LAMP
          (iii) Role of gene in stress condition and                      technology (Linux, Apache, MySQL, PHP). Out of 259
references.                                                               genes collected from all available sources like NCBI,
          If information about any field was not available,               EMBL and DDBJ; 237 are known for coding proteins.
then NA (Not Available) was written in corresponding                      Maximum numbers of genes were found in Glycine max
column.                                                                   (62) with a minimum of 02 in Arachis hypogaea. In
          Any gene can be searched into database through                  addition, 42 ESTs were collected for Phaseolus vulgaris.
three different keywords i.e. by species name, gene name                  These genes respond to various stress conditions. Among
or by stress condition in which they are involved.                        all the stress conditions, largest number of genes were
Database also includes information about 42 ESTs for                      found for oxidative stresses. A large number of genes
Phaseolus vulgaris. A separate web page was designed                      were also found for salt stress. The database includes

                                       VOL. 1, NO. 1, November 2011                                          ISSN XXXX-XXXX
                                        ARPN Journal of Science and Technology
                                            ©2011-2012 ARPN Journals. All rights reserved.

various keywords like species name, gene name and                         REFERENCES
stress condition to extract information. Information on
orthologs and paralogs of proteins coded by stress                        [1] Khan N A and Singh S 2008 Abiotic stress and plant
related genes is also available. These orthologs and                          responses. I.K. International Pub. House. ISBN:
paralogs can be searched out by using protein number as                       9788189866952
keyword. Link to other useful databases related to plant
species, stress condition and orthology and paralogy is                   [2] Fujita M et al 2006 Crosstalk between abiotic and
also provided. Proteins of G. max, P. glaucum, P.                             biotic stress responses: a current view from the
vulgaris, S. officinarum and Z. mays do not have any                          points of convergence in the stress signaling
orthologs or paralogs sequences. Paralogs sequences                           networks. Curr Opin Plant Biol 9 436-442
were available only for A. thaliana and H. vulgare. A                     [3] Cochrane G R and Galperin M Y 2010 The 2010
user-friendly web interface was designed for this                             Nucleic Acids Research Database Issue and online
database to make it platform-independent and easily                           Database Collection: a community of data resources.
accessible.                                                                   Nucleic Acids Res 38 D1-D4.
          Practical implications of this database lay in the
wealth of information on plant stress related genes. This                 [4] Wanchana S et al 2008 The Generation Challenge
easily accessible database may serve as a potential tool                      Programme comparative plant stress-responsive
for researchers due to the information it contains on                         gene catalogue. Nucleic Acids Res 36 D943-D946.
stress related genes having impact on crop productivity
and defence system of plants.

        This work was supported by Department of
Biotechnology-Centre Of Excellence (DBT-COE)


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