Biosci. Biotech. Res. Comm. 11(3): 476-480 (2018)
Phylogenetic analysis of target of rapamycin (TOR)
kinase gene of some selected plants species
Swapnil Sapre, Sharad Tiwari and Vishwa Vijay Thakur
Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur 482004, India
TOR kinase has been reported to regulate number of biological processes, including central dogma, which collectively
contributes to cell growth in all the organisms. The major role of the target of rapamycin (TOR) kinase is to encour-
age cell growth in response to favorable conditions. Up to some extent,nucleotide and amino acidsequencesof TOR
kinase were found to be similar in all the organismswherein it has been identi ed or characterized.In order to assess
the phylogenetic relationship and conservative nature of TOR gene among 32 different plants species TOR gene
sequences and protein sequence retrieve from public repository database NCBI.Sequence length and GC% of each
sequence were determined. Maximum GC% was found in TOR kinase gene of Brachypodium distachyon (46.18%). All
the 32 TOR gene sequences contained more than 43% of GC. Phylogenetic tree constructed using Neighbor-joining
method separated TOR kinase into two distinct groups i.e. monocots and dicots. Sequences of TOR kinase from similar
family of plants were grouped together signifyingits conserved nature within the family. The phylogenetic tree of
TOR gene at both nucleotides and proteins level from different species perfectly re ects phylogenetic relationships of
the species. This strong conservation of tor genes among all the species including in this investigation advocate the
general signi cance of this kinase and, consequently, the entire TOR pathway.
*Corresponding Author:
Received 20
April, 2018
Accepted after revision 21
July, 2018
BBRC Print ISSN: 0974-6455
Online ISSN: 2321-4007 CODEN: USA BBRCBA
Thomson Reuters ISI ESC / Clarivate Analytics USA and
Crossref Indexed Journal
NAAS Journal Score 2018: 4.31 SJIF 2017: 4.196
© A Society of Science and Nature Publication, Bhopal India
2018. All rights reserved.
Online Contents Available at: http//
DOI: 10.21786/bbrc/11.3/17
The modulation of growth rate in a particular environ-
mental condition such as nutrient availabilityis neces-
sary for continued existence. Plant growth is largely
dependent on surrounding environmental information.
It includes cell growth coupled with cell proliferation
and cell expansion depends onexogenous factors such
as stresses and nutrient availability. Unlike animals,
in plants, postembryonic growth is directly in uenced
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.
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
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.
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
Swapnil Sapre et al.
FIGURE 1. Phylogenetic tree showing the relation-
ships between TOR nucleotide sequences from differ-
ent plants.
sequences,all belongs to Poaceae family. In this group
the plant species of genus Oryza is closely related with
Bracypodiumdistachyon while Zeamay sexhibited higher
similarity with plant species Sorghum bicolor and Setaria
italica. In group II, all the sequences of TOR kinase gene
of dicot plants clustered into 5 subgroups. TOR gene
sequence of Beta vulgaris was lone species in subgroup
II-a whereas, remaining 4 subgroups clustered according
to their family such as subgroup II-b consist of 5 spe-
cies of Solanaceae, Subgroup II-cwas occupied bythe 4
species of Brasicaceae while 6 species of Fabaceae fam-
ily gathered in subgroup II-d. On the other hand,  ve
families namely Euphorbiacea, Malvaceae, Rootaceae,
Rosaceae and Vitaceae grouped into subgroupII-e.
Inphylogenetic tree of amino acid sequences of TOR
kinase divided into two groups of monocots and dicots
(Fig 2) with a similar clustering pattern to nucleotide
sequenc eexcept Vitis vinifera which formed a separate
group II-d in phylogenetic tree of protein sequences. In
group I of monocots, two subgroups of 7 and 3 plants
FIGURE 2. Phylogenetic tree showing the relation-
ships between TOR protein sequences from different
were formed. In group II of dicots, six subgroups were
formed. Vitis vinifera and Beta vulgaris fell into two
separate groups whereas, other groups contained 4,5
and 6 species of Brasicaceae, Solanaceae and Fabaceae
respectively whereas, 5 genera clustered inII-e. Above
mentioned results showed the highly conserved nature
of TOR gene among different plant species at fam-
ily level. The results obtained are in accordance with
previous research  nding reported by John et al. (2011)
as they observed similar pattern of clustering during
phylogenetic analysis of TOR proteins of different spe-
cies included animal kingdom, fungi, algae and higher
plants. In higher plants all the studied plants species
are separated into two cluster i.e. monocots and dicots.
The plants species Oryzasativa, Sorghum bicolor and
Zea mays clustered together exhibited the similarity of
results obtained during present studies. The amino acid
sequences were found to be conserved among a wide
variety of plants including all the cereals andin many
dicots. Our results are also supported by another inves-
tigation carried out by Dobrenel et al. (2011) in which
protein sequences of TOR kinase from plants, animals,
yeasts, algae and moss were aligned and monocots and
dicotsgrouped in separate clusters. The plants species
Swapnil Sapre et al.
Table 1. List of source plants of tor genes utilized in investigation and their features
Plant Accession number Family Size (bp) GC%
Zea mays NM_001111823 Poaceae 7691 44.80
Nicotiana sylvestris XM_009797907 Solanaceae 6552 43.86
Setaria italica XM_004962286 Poaceae 7899 45.80
Sorghum bicolor XM_002439595 Poaceae 7544 44.55
Brachypodium distachyon XM_003568577 Poaceae 8263 46.18
Oryza sativa XM_015784081 Poaceae 7659 45.05
Oryza brachyantha XM_006654108 Poaceae 7708 44.75
Oryza sativa AB982929 Poaceae 7398 44.59
Elaeisguineensis XM_010938396 Arecaceae 7722 44.28
Musa acuminata XM_009396742 Musaceae 7722 44.51
Vitisvinifera XM_002275555 Vitaceae 7791 44.15
Phoenix dactylifera XM_008784352 Arecaceae 3530 43.63
Ricinuscommunis XM_015718655 Euphorbiaceae 7993 43.69
Arachisipaensis XM_016346885 Fabaceae 8105 44.45
Nicotiana tabacum NM_001325223.1 Solanaceae 7488 44.78
Solanum tuberosum XM_006346213.2 Solanaceae 7929 43.93
Capsicum annuum XM_016726515.1 Solanaceae 7581 44.00
Citrus sinensis XM_006486806.2 Rutaceae 7929 43.65
Nicotiana tomentosiformis XM_009629165.1 Solanaceae 6982 43.81
Jatropha curcas XM_012237807.1 Euphorbiaceae 6910 43.14
Gossypiumhirsutum XM_016860166.1 Malvaceae 7904 44.00
Arachisduranensis XM_016109414.1 Fabaceae 8144 44.51
Prunusmume XM_008238021.2 Rosaceae 7991 44.50
Glycine max XM_003538286.3 Fabaceae 8287 42.97
Vigna radiata XM_014665082.1 Fabaceae 8372 43.11
Cicer arietinum XM_004511268.2 Fabaceae 8411 42.42
Beta vulgaris XM_010693230.1 Amaranthaceae 8031 43.71
Brassica rapa XM_009149609.1 Brassicaceae 7800 44.44
Brassica napus XM_013786769.1 Brassicaceae 7581 44.60
Brassica napus XM_013893643.1 Brassicaceae 7880 44.37
Brassica oleracea XM_013736055.1 Brassicaceae 7630 44.39
Phaseolus vulgaris XM_007157127.1 Fabaceae 4186 43.17
Oryza sativa subsp. Japonica, Oryza sativa subsp. Indica,
Bracypodiumdistachyon, Sorghum bicolor and Zea May-
sare grouped together and formed the separate cluster
of monocot species which showed similarity with results
obtained during present investigation.
During phylogenetic analysis and sequence similar-
ity search of wheat TOR gene with other plant species
Sapre et al. (2016) observed the same clustering pat-
tern of plant species as obtained in this investigation.
The results of this investigation are not contradicted
the results obtained by Nanjareddy et al. (2016) during
the phylogenetic analysis of bean TOR gene which con-
rmed that this gene belongs to the legume group and
is closely related to the G. max and M. truncatula TOR
genes which showed the highly conserved nature of TOR
gene at family level. In our studies all the plants species
including in present investigation are clustered together
according to their family showed the similar nature of
gene as mentioned by Nanjareddy et al. (2016).
During present investigation phylogenetic analysis was
carried out separately among TOR kinase gene sequences
and amino acid sequences of 32 plants retrieve from pub-
lic repository database NCBI. The phylogenetic tree of
Swapnil Sapre et al.
TOR gene and its homolog’s from several plants includ-
ing both monocots and dicots revealed a close relation-
ship between plant species.All sequences were grouped
separately in two groups i.e. monocots and dicots. Fur-
ther, sequences from similar family grouped together
perfectly re ect the conserve nature of TOR kinase gene
at nucleotide and protein sequence level.This strong
conservation of TOR geneamong all the studied plant
speciesadvocates the general signi cance of this kinase
and, consequently,the entire TOR pathway.
Ahn CS, Han JA, Lee HS, Lee S, Pai HS (2011) The PP2A regula-
tory subunit Tap46, a component of the TOR signaling path-
way, modulates growth and metabolism in plants. Plant Cell
Creff A, Sormani R, Desnos T (2010) The two Arabidopsis RPS6
genes, encoding for cytoplasmic ribosomal proteins S6, are
functionally equivalent. Plant Mol. Biol. 73: 533-546
Dobrenel T, Marchive C, Azzopardi M, Clément G, Moreau M,
Sormani R, Robaglia C, Meyer C (2013) Sugar metabolism and
the plant target of rapamycin kinase: a sweet operaTOR? Front.
Plant Sci. 4: 93
Dobrenel T, Marchive C, Sormani R, Moreau M, Mozzo M,
Montane M, Menand B, Robaglia C, Meyer C (2011) Regulation
of plant growth and metabolism by the TOR kinase. Biochem.
Soc. Trans.39:477-481
Felsenstein J (1985) Con dence limits on phylogenies: An
approach using the bootstrap. Evolution 39:783-791
Hall TA (1999) BioEdit: a user-friendly biological sequence
alignment editor and analysis program for Windows 95/98/NT.
Nucleic Acids Symp. Ser. 41:95-98
John F, Rof er S, Wicker T, Ringli C (2011) Plant TOR signaling
components. Plant Signal. Behav. 6:1700-1705
Moreau M, Azzopardi M, Clement G, Dobrenel T, Marchive C,
Renne C, Martin-Magniette ML, Taconnat L, Renou JP, Roba-
glia C, Meyer C (2012) Mutations in the Arabidopsis homolog
of LST8/GbL, a partner of the target of Rapamycin kinase,
impair plant growth,  owering, and metabolic adaptation to
long days. Plant Cell 24:463-481
Nanjareddy K, Blanco L, Arthikala MK, Alvarado-Affantranger
X., Quinto C, Sanchez F, Lara M (2016) A legume TOR protein
kinase regulates rhizobium symbiosis and is essential for infec-
tion and nodule development. Plant Physiol. 172:2002-2020
Ren M, Venglat P, Qiu S, Feng L, Cao Y, Wang E, Xiang D,
Wang J, Alexander D, Chalivendra S, Logan D, Mattoo A, Sel-
varaj G, Datla R (2012) Target of rapamycin signaling regulates
metabolism, growth, and life span in Arabidopsis. Plant Cell
24: 4850-4874
Robaglia C, Thomas M, Meyer C (2012) Sensing nutrient and
energy status by SnRK1 and TOR kinases. Curr. Opin. Plant
Biol. 15:301-307
Sapre S, Tiwari S, Thakur VV, Tripathi N (2016) Molecular
characterization and sequence identi cation of TOR kinase
gene from wheat (Triticum aestivum). Adv. Life Sci. 5(12):
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S
(2011) MEGA5: Molecular evolutionary genetics analysis using
maximum likelihood, evolutionary distance and maximum
parsimony methods. Mol. Biol. Evol.28:2731-2739
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W:
improving the sensitivity of progressive multiple sequence
alignment through sequence weighting, position-speci c gap
penalties and weight matrix choice. Nucl. Acids Res. 22:4673-
Xiong Y, Sheen J (2012) Rapamycin and glucose-target of
rapamycin (TOR) protein signaling in plants. J. Biol. Chem.
287: 2836-2842
Yuan HX, Xiong Y, Guan KL (2013) Nutrient sensing, metabo-
lism and cell growth control. Mol. Cell 49: 379-387