Prediction of lactoferrin like proteins from plant resources
*SHASHANK R1, RAGHVENDAR S2, AND SHRIKANT S1
1. School of Life Science, Singhania University, Jhunjhunu, (RJ); 2. Bioinformatics Facility,
Department of Biotechnology, Sardar Vallabh Bhai Patel University of Agriculture & Technology.
Meerut (U.P.)
* = Corresponding author
Research scholar
Bioinformatics facility,
Sardar Vallabh Bhai Patel University of
Agriculture & Technology
Meerut (U.P.)
Mob- +919286397873
E-mail: - shashank.bioinfo@gmail.com
Prediction of lactoferrin like proteins from plant resources
1. School of Life Science, Singhania University, Jhunjhunu, (RJ); 2. Bioinformatics Facility,
Department of Biotechnology, Sardar Vallabh Bhai Patel University of Agriculture & Technology.
Meerut (U.P.)
Abstract
In silico study was conducted to analyse lactoferrin [Homo sapiens] like molecules from five
different plant families, bacteria and algae database using NCBI. The Basic Local Alignment
Search Tool (BLAST) was used to calculating sequence similarity by applying BLASTp to
search protein database against protein query followed by BL2seq for finding out similarity
between query and subject sequences. On the basis of e-value, bit score and identities, it was
observed that sequence establish resemblance with lactoferrin like protein from Algae named
Dunaliella salina, Euphoribaceae named Ricinus communis and from other animal sources as
whey and iron binding proteins.
Keywords: LTF, Blastp, Structure, bl2seq, E-value, Plant resources
Introduction
Lactoferrin (LF) is an iron-binding protein from milk, structurally similar to the transferrins. So it
is also known as lactotransferrin (LTF) is a globular multifunctional protein with antimicrobial
activity (bacteriocide, fungicide) and is part of the innate defense, mainly at mucoses (Ward, et.
al., 2006). Lactoferrin is also present in secondary granules of PMN and also is secreted by some
acinar cells. Lactoferrin can be purified from milk or produced recombinantly. Human colostrum
has the highest concentration, followed by human milk, then cow milk. For better prospective of
commercial application of lactoferrin protein, it is necessary to define the lactoferrin resource in
plant and likewise other resources. So, the study was carried out with objectives to predict the
homology of lactoferrin [Homo sapiens] with possible sources of different plant families, bacteria
and algae.
Material and method
In present work, we use BLASTp, BL2seq for carried out our work. Basic Local Alignment
Search Tool (BLAST) is the tool most frequently used for calculating sequence similarity.
BLAST comes in variations for use with different query sequences against different databases.
BLASTp was used for search protein database against protein query. On the other hand, BL2seq
was used for finding out similarity between two sequences (query and subject sequences.).
We deposit the lactoferrin sequence retrieved from NCBI, into the BLASTp search box
and set the plant/protein name against which, we try to find out the similarity against query
sequence. Then select the best similarity from the results illustrate by BLASTp database search
on the bases of e-value and bit score as higher bit score and lowest e- value describe best result.
Following that, the selected subject sequence was submitted to BL2seq search box along with
query sequence.
Results and Discussion
The data available from different plant families (Apiaceae, Bambuseae, Euphorbiaceae, Palmae
and Rutaceae), algae, bacteria, whey proteins and iron binding proteins was analyzed and the
results are given in Table No-1. On the basis of above converse approach, It showed that
lactoferrin protein [Homo sapiens] Query Sequence-1 has vast relationship with plant and other
resources also. On the basis of e-value (1e-37) and bit score (156 bits (394)) and 178/666 (26%)
identities, LTF sequence establishes resemblance with transferrin-like protein from Dunaliella
salina, an Algae. Yet again, LTF harmonized with Iron binding protein from Chrysemys scripta
elegans, demonstrate the e-value and bit score are 0.0 and 742 bits (1915) respectively also with
identity of 386/717 (53%). In Struthio camelus illustrate 0.0 e- value bit score 716 bits (1847)
and identity362/718 (50%), in iron binding protein from Meleagris gallopavo represent the 0.0
e- value with 686 bits (1771) bitscore and identity 368/721 (51%) .Lytechinus variegatus (major
yolk protein) initiate 94.7 bits (234) bit score 136/593 (22%) identity and 5e-21 e-value, Ricinus
communis a member of Euphorbiaceae family found similarity score 71.6 bits (174), e-value 1e12 and percent identity 42/133 (31%) (Table1.1). Further we have confirmation our result by
using Blast2 between human lactoferrin sequence and sequences from above stated organisms.
Iron binding proteins covered 99% human lactoferrin with 0.0 E-value. On the other hand
Lytechinus variegatus covered 94% with e- value 2e-23; Ricinus communis covered 36% with
e- value 1e-36, Dunaliella salina covered 80% with e- value 6e-41of human lactoferrin (Table
1.2).
Query Sequence- 1: Lactoferrin protein [Homo sapiens]
>gi|187122|gb|AAA59511.1| lactoferrin [Homo sapiens]
MKLVFLVLLFLGALGLCLAGRRRRSVQWCAVSQPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQAIA
ENRADAVTLDGGFIYEAGLAPYKLRPVAAEVYGTERQPRTHYYAVAVVKKGGSFQLNELQGLKSCHTGLR
RTAGWNVPIGTLRPFLNWTGPPEPIEAAVARFFSASCVPGADKGQFPNLCRLCAGTGENKCAFSSQEPYF
SYSGAFKCLRDGAGDVAFIRESTVFEDLSDEAERDEYELLCPDNTRKPVDKFKDCHLARVPSHAVVARSV
NGKEDAIWNLLRQAQEKFGKDKSPKFQLFGSPSGQKDLLFKDSAIGFSRVPPRIDSGLYLGSGYFTAIQN
LRKSEEEVAARRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDEGYVY
TAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTSLTWNSVKGKKSCHTAVDRTAGWN
IPMGLLFNQTGSCKFDEYFSQSCAPGSDPRSNLCALCIGDEQGENKCVPNSNERYYGYTGAFRCLAENAG
DVAFVKDVTVLQNTDGNNNEAWAKDLKLADFALLCLDGKRKPVTEARSCHLAMAPNHAVVSRMDKVERLK
QVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTS
PLLEACEFLRK
Table 1.1: Description of best matched proteins/plant resources with lactoferrin
Table 1.2 Bl2seq of Homo sapiens against different plants, algae and iron binding
proteins/whey proteins
Conclusion
Lactoferrin is significant component of milk and play an important role in iron binding. As milk
resources are reducing day by day it is necessary to find out the optional resources for the same and
possibly plant will be the good resource for the same. Expression of recombinant human milk
proteins in rice is realistic and a possibility for the addition of bioactive factors to infant formula
and baby foods; Lonnerdal (2002) was successfully produce several such proteins at very high
expression levels and have shown that the transmission is stable through several generations.
Rachmawati et al. (2005) studied the expression and characteristic of recombinant human
lactoferrin (rhLF) in the transgenic Javanica rice cv Rojolele obtained through Agrobacteriummediated transformation. Transgenic rice produced considerable amount of the recombinant hLF in
its seed. The efficiency of glutelin signal peptide and hLF signal peptide in the rhLF expression is
almost same. Although the exact mechanism is unknown, the expression of rhLF was localized into
the intracellular of endosperm. Present study may be helpful to the researchers as we find the
significant results for LTF in iron binding proteins, plants, algae and whey proteins. On the bases of
covered area of sequences and similarity found by blastp and bl2seq stated in results, lactoferrin
may be produced commercially from plant and likewise resources.
References
1. Ward P P, Paz E, and Conneely O M (2006) Multifunctional roles of lactoferrin: a
critical overview. Cellular & Molecular Life Science 62( 22): 2540-2548.
2. Rachmawati D, Mori T, Hosaka T, Takaiwa F, Inoue E and Anzai H(2005) Production
and characterization of recombinant human lactoferrin in transgenic javanica rice.
Breeding Science 55: 213-222.
3. Lonnerdal B (2002). Expression of Human Milk Proteins in Plants. Journal of the
American College of Nutrition, 2:218S-221S.
4. www.ncbi.nlm.nih.gov/blast.cgi
5. www.ncbi,nlm.nih.gov/