Swapnil Sapre et al.
plant species using BLASTn (http://www.ncbi.nlm.nih.
gov/BLAST/). TOR gene nucleotide sequences of differ-
ent plants were selected on the basis of E-value (within 0
to 1e – 50). DNA sequences were aligned with ClustalW
(Thompson et al. 1994) and alignments were subse-
quently adjusted manually using BioEdit (Hall, 1999).
Sequence length and GC% of each sequencewas calcu-
lated by MEGA6 (Tamura et al. 2011). Protein sequences
were also deduced from all retrieved sequences of TOR
kinase genes and were aligned using ClustalW and go
for construction of phylogenetic tree.
To evaluate the genetic relationship between retrieved
nucleotide sequences of TOR kinase gene, a phyloge-
netic tree was constructed using Neighbor-joining (NJ)
method. The output data was processed using MEGA 6
to draw the phylogenetic tree. The bootstrap consensus
tree (Felsenstein, 1985) inferred from 1000 replicates
was selected to represent the evolutionary history of the
32 TOR kinase genes under study. Phylogenetic tree was
also constructed for amino acid sequences of TOR kinase
genes two know the sequence homology at protein level.
RESULTS AND DISCUSSION
In this study, TOR kinase gene sequences of 32 plants
species belongs to 11 familieswere selected and retrieved
from GenBank for phylogenetic analysis. The sequence
lengths of all the TOR genes with GC% are given in
Table 1. Maximum GC% was found in TOR kinase gene
of Brachypodium distachyon (46.18%). All the 32 TOR
gene sequences containedmore than 43% of GC.
The evolutionary relationships between the plants
were evaluated by phylogenetic analysis of the aligned
nucleotides and amino acids sequence of their TOR kinase
gene. TOR kinase gene sequences currently available
in the database are either full length mRNA sequences
or predicted sequences obtained from annotation of
genome. The phylogenetic tree obtained by Neighbor-
joining method showed two distinctphylo-groups of
TOR kinase genes from monocots and dicots (Fig 1).
Group I containing only monocots included Zea mays,
Setaria italica, Sorghum bicolor, Brachypodium dis-
tachyon, Oryza sativa, Oryza brachyantha, Phoenix dac-
tylifera, Elaeis guineensis and Musa acuminate. Cluster
of monocots further divided in two subgroups, wherein
subgroup I-acontained three gene sequences, two from
family Arecaceae and one from family Musaceae. The
plant species Elaesis guineensis and Phoenixdactylifera
belongs to same family Arecaceae and also exhibited
high degree of similarity than plant species Musaacumi-
nata belongs to family Musaceae in subgroup I-a.
This result also revealed that the relatedness of these
two families were higher than the other family included
in the present studies. While, subgroup I-b comprised 7
by availability of nutrients and energy source that are
present outwardly or generated by various cellular pro-
cesses (Nanjareddy et al. 2016). However, so far, very
few secrets have been revealed on mechanism that how
this information is perceived and transduce into coher-
ent growth and developmental decisions.One of the most
important pathways that are found in all eukaryotes is
the one related to the target of rapamycin (TOR) protein
kinase.
The target of rapamycin (TOR), a Ser/Thr protein
kinase, has emerged as a key player of nutrient, energy,
and stress signaling networks (Dobrenel et al. 2013;
Yuan et al. 2013). It is a large protein that belongs to the
phosphoinositide 3-kinase-related kinase family and is
highly conserved among all eukaryotes (Robaglia et al.
2012). Numerous components of the TOR signalingma-
chinery have beenidenti ed in model plant Arabidopsis.
Various members of the TOR complex such as the RAP-
TOR1/RAPTOR2, LST8-1/LST8-2, S6K1/S6K2, ribosome
protein small subunit6 (RPS6A/B), type 2A-phosphatase-
associated protein 46 kD (TAP46), and ErbB-3 epider-
mal growth factor receptor binding protein have been
reported in photosynthetic eukaryotes through sequence
homology searches from C. reinhardtii to Arabidopsis
plants (Creff et al. 2010; Ahn et al. 2011; Moreau et al.
2012; Ren et al. 2012; Xiong and Sheen, 2012).
In this era of high throughput gene and genome
sequencing, prediction of function of a gene is a key
step. Various reverse genetics techniques like site directed
mutagenesis and RNAi are effective to solve this purpose.
Another easier way to predict function of a particular
gene and phylogenetic relation between different species
iswith the use of bioinformatics. Nowadays, increasing
sequenced genomesof diverse plants are providing new
opportunities to study gene families in an evolution-
ary context. Based on these facts, present investigation
was conducted to evaluate the phylogenetic relationship
and sequence similarity of TOR kinase genes from dif-
ferent plants species and make an efforts to know the
conserve nature of TOR gene at both nucleotide and pro-
tein sequence level. Phylogenetic tree analysis on basis
of conserved nature and similarity of known sequence
helps us to predict the function of a gene and also exhibit
the phylogenetic relationships of the species (John et al.
2011). However, for a deeper understanding of the gene
function, it is helpful to go beyond cataloguing of simi-
larities and differences and to understand how and even
why these similarities and differences arise.
MATERIAL AND METHODS
Nucleotide sequence of TOR kinase gene of Zea mays
was retrieved from NCBI database for its further use
as bait sequence to isolate other sequences of different
BIOSCIENCE BIOTECHNOLOGY RESEARCH COMMUNICATIONS PHYLOGENETIC ANALYSIS OF
TOR
KINASE GENE IN PLANTS 477