In silico identification of conserved proteins in sequenced
chloroplast genomes of C3 plants
Dhwani Raghav, Asheesh Shanker and Vinay Sharma
Department of Bioscience and Biotechnology
Banasthali University, Rajasthan-304022
Corresponding author’s Email: sasheesh@bv.banasthali.ac.in
Abstract
Chloroplasts are the organelles that capture light energy to conserve it in the form of ATP and reduce
NADP to NADPH through a complex set of processes called photosynthesis. The chloroplast genome was
the first plant genome characterized. A large number of databases (NCBI, EMBL, DDBJ) were created to
store sequences of various genomes.These databases also contains tools to analyze these sequences. Using
BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST), conserved and unique proteins between different
species of C3 plants, namely Atropa belladonna, Cucumis sativus, Glycine max, Gossypium hirsutum and
Lotus japonicus were identified. Conserved proteins play an important role in phylogenetic analysis, while
unique proteins provide a new shed of light in the field of functional and comparative genomics.
1. INTRODUCTION
The chloroplast is the hallmark organelle of
plants (Gr. Chloros means green and plastos
means formed). These specialized organelles are
one of the many unique cells in the body and are
generally considered to be originated
endosymbiotically [12]. Chloroplasts contain the
chlorophyll, hence provide the green color and
used for critical functions such as
photosynthesis, starch synthesis, nitrogen
metabolism, sulfate reduction, fatty acid
synthesis, DNA and RNA synthesis [17], and are
also involved in the energetic processes in plants
[9].
Chloroplasts have their own DNA which
resembles large bacterial plasmids or small
chromosomes and it inherited cytoplasmically,
independent of nuclear genes [16]. Its small size
ranges from about 120-220 kb with 120-150
genes [14] and limited number of repeated
elements made it a prime candidate for
characterization. The gene content and
arrangement of chloroplast DNAs (cpDNAs) in
higher plants are relatively uniform from species
to species. Its abundance in foliar tissue made it
easy to isolate. The inverted repeat is an
interesting feature of the chloroplast genome.
Completely sequenced chloroplast genomes
provide a rich source of data that can be used to
find phylogenetic relationship [4].
C3 plants are those in which C3 carbon fixation
takes place, which is a pathway for carbon
fixation in photosynthesis. In this process carbon
dioxide and ribulose bisphosphate (RuBP, a 6carbon sugar) is converted into
phosphoglycerate, which is a 3- carbon
compound. Melvin Calvin and his coworkers at
the University of California worked out the
mechanism of the reduction of CO2 and
suggested cyclic pathways where the first stable
compound produced during carbon reduction is a
3-C compound, i.e., 3-phosphoglyceric acid. In
C3 plants, carbon fixation and photosynthesis
happens in mesophyll cells just on the surface of
the leaf.
Using bioinformatic tools to compare important
species is now feasible and structural genomics
continue in importance and establishment of
structure-function relationships become a
common way of comparative analysis. Inference
of relationships from proteins of known function
to proteins of unknown function that are
structurally similar can be established through
comparative analysis [6]. The smallness in size
of chloroplast genomes facilitates for the
discovery of disease resistance genes,
introgression of important traits in transgenic
plants quantitative trait analysis [11], and
phylogenetic studies [4] etc.
The Chloroplast Genome Database (CGD;
ChloroplastDB) [3] is an interactive, web-based
database for fully sequenced plastid genomes,
containing genomic, protein, DNA and RNA