Clustral W2

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MULTIPLE CLUSTRAL ALIGNMENT OF HUMAN P27 PEPTIDE SEQUENCE WITH FIVE OTHER SPECIES OF DIFFERENT PHYLA, FIVE HOMOLOGUES FROM CLOSELY RELATED SPECIES AND ONE PARALOGUE (VARIANT)

INTRODUCTION

Bioinformatics is the branch of life science dealing with the computational analysis of biological data. With the help of bioinformatics tools, data obtained from molecular biology can be analysed to understand the genotype and phenotype of an organism.

Clustral W2 is an automatic program for global multiple alignment of protein (or DNA) sequences. Global alignment involves entire sequence where there is the need to show gaps representing insertions and/or deletions. The alignments obtained from Clustral W2 are progressive. They consider the sequence redundancy. Thus Clustral W2 is used to do multiple sequence alignment for DNA and protein producing biologically meaningful alignments of different sequences. The main aim of this tool is to calculate the best match of the selected sequences and to align them to reveal identities, similarities and the differences between the sequences. Additionally, evolutionary relationship between the selected sequences can be seen in phylograms by using Clustral W2 program. (European Bioinformatics Institute, 2009)
For the identification of conserved sequence regions in different species, multiple alignments of protein sequences are very essential. This enables us to modify the function and to predict the structure of a protein. Similarly, it helps to identify a new member of protein family. (European Bioinformatics Institute, 2009)

Cyclin-dependent kinase inhibitor 1B is a protein in the form of enzyme in human body which is encoded by the CDKN1B gene. (Polyak K et al, 1994) This protein is also known as human p27 and belongs to theCip/Kip family of cyclin dependent kinase (Cdk) inhibitors.It has wide range of tissue specificity , however present mainly in liver and kidney. It is found predominantly in quiescent cells. The main function of p 27 is to bind with cyclin E-CDK2 or D-CDK4 complexes and prevent their activation. Since E-CDK2 and D-CDK4 are the up regulators of cell cycle, p 27 plays the role of cell cycle inhibitor at G1. This protein can induce cell cycle arrest and serve as tumor suppressors (Chen J et.al, 2009)

This practical has been aimed to take p 27 peptide sequences of human and 5 other species of different phylum. Then sequences will be kept in multi-sequence alignment using clustral W2. After that same process will be repeated by taking homologues of p 27 from very closely related species. Finally a paralogue or variant of human p 27 will be taken and will be aligned with wild type human p 27.

AIM

1. To take p 27 peptide sequences of human and 5 other species of different phylum, followed by clustral W2 alignment of these peptide sequences.
2. To take homologues of human p 27 peptide sequence from 5 closely related species, followed by clustral W2 alignment of these peptide sequences .
3. To take a variant of human p 27 sequence and clustral W2 alignment of these peptide sequences.
4. To analyze critically regarding clustering, homology, identity, conservation, divergence and gaps in the sequences and the potential implications.

MATERIALS AND METHODS

The peptide sequence of p 27 of Homo sapiens and other organism like Mycobacterium bovis, Haemophilus ducreyi, Brugia malayi, and HTLV-1, which do not belong the phylum chordata, were taken from NCBI database at http://www.ncbi.nlm.nih.gov/ . These peptide sequences were then entered in Clustral W2 (www.ebi.ac.uk/Tools/clustalw2/index.html) to get score table and global alignment. After that again NCBI database was used to retrieve five homologues of human p 27 from closely related organisms. At this stage, p 27 peptide sequences of five chordates namely pig, bovin, felca (cat), cafna (dog) and crigr(Chinese hamster) were taken. These sequences were also aligned by Clustral W2 alignment and the results were analysed. Finally, paralogue or variant sequence of human p27, obtained from NCBI, was a aligned with wild type human p 27 , and the results were analysed.

RESULT

CLUSTRAL ALIGNMENT OF P 27 PEPTIDE SEQUENCES OF HUMAN, MYCOBACTERIUM, HAEMOPHILUS, BRUGIA AND HTLV-1
Mycobaceria, Haemophilus, Brugia, and HTLV-1 are microorganisms belonging to different phyla respectively. Phylogenic tree shows that they are very distantly related to human beings. Following are the sequences of p 27 peptide sequences of these organisms obtained from NCBI:
>human p27

MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDVS GSRPAAPLIG
APANSEDTHL VDPKTDPSDS QTGLAEQCAG IRKRPATDDS STQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRRRQT

>Mycobacterium bovis p27
1 mpnfwalppe instriylgp gsgpilaaaq gwnalasele ktkvglqsal dtllesyrgq
61 ssqaliqqtl pyvqwlttta ehahkiaiql taaanayeqa raamvppamv ranrvqttvl
121 kainwfgqfs triadkeady eqmwfqdalv menyweavqe aiqstshfed ppemaddyde
181 awmlntvfdy hnenakeevi hlvpdvnker gpielvtkvd kegtirlvyd geptfsykeh
241 pkf

>Haemophilus ducreyi p27
1 mtkftkisaa alfalfltac dkpannpvet kpaataatqp eadkkveakm dtgaedykkf
61 qewqqnqekl igeainnele klgeekakde tlvqdtvnna ildqiekiqq naksleikde
121 qikvlkeksl eamalgakmi kqnselaknp tpeaqkafse lqvqldkiaa dgqtieaeln
181 kkygistpve atiptinpde ipeedeeeed enk

>Brugia malayi p27
1 kmqrerkidv tpsnysvldt efgsmrerfe temrhveeem krlrrefegy tpsqpgsqvd
61 nrsttyhree srryessstq gsgppppsst frseggfgrp dmmsirptyd pylenlkspl
121 ikdesdgktl rlrfectvqp eevtvktvdn rllvrakhee ktpqravfre ynqefmlprg
181 tnpelisstl stdgvltvea plphlaiqh

>HTLV-1 p27
1mpktrrrprr sqrkrpptpw ahfpgfgqsl lfgypvyvfg dcvqgdwcpi sgglcsarlh
61 hallatcpe hqitwdpidg rvigsalqfl iprlpsfptq rtsktlkvlt ppithttpni
121sflqamrk yspfrngyme ptlgqhlptl sfpdpglrpq nlytlwggsv vcmylyqlsp
181 twpllphv ifchpgqlga fltnvpykri eellykislt tgaliilped clpttlfqpv
241pvtltawq nasfrstqps plqalfghlp marl

When the peptide sequences from figure 1 , 2 , 3, 4 and 5 were analysed by clustral W2, following results were obtained:
Table1. : Scores Table obtained from Clustral W2 showing different score values
SeqA Name Len(aa) SeqB Name Len(aa) Score
==============================================
1 human 198 2 Mycobacterium 243 2
1 human 198 3 Haemophilus 213 9
1 human 198 4 Brugia 209 5
1 human 198 5 HTLV-1 272 3

Mycobacterium MPNFWALPPEINSTRIYLGPGSGPILAAAQGWNALASELEKTKVGLQSALDTLLESYRGQ 60
HTLV-1 MPKTRRRPRRSQRKRPPTPWAHFPGFGQSLLFGYPVYVFGDCVQGDWCPISGGLCSARLH 60
Brugia --------KMQRERKIDVTPSNYSVLDTEFGS------MRERFETEMRHVEEEMKRLRRE 46
Haemophilus ---------MTKFTKISAAALFALFLTACDKP------ANNPVETKPAATAATQPEADKK 45
human ----------MSNVRVSNGSPSLERMDARQAE--------HPKPSACRNLFGPVDHEELT 42
.

Mycobacterium SSQALIQQTLPYVQWLTTTAEHAHKIAIQLTAAANAYEQAR-----AAMVPPAMVRANRV 115
HTLV-1 RHALLATCPEHQITWDPIDGRVIGSALQFLIPRLPSFPTQRTSKTLKVLTPPITHTTPNI 120
Brugia FEGYTPSQPGSQVDNRSTTYHREESRRYESSSTQGSGPPPP--------SSTFRSEGGFG 98
Haemophilus VEAKMDTGAEDYKKFQEWQQNQEKLIGEAINNELEKLGEEK--------AKDETLVQDTV 97
human RDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGS--------LPEFYYRPPRP 94

Mycobacterium QTTVLKAINWFGQFSTRIAD-----------------KEADYEQMWFQDALVMENYWEA- 157
HTLV-1 PPSFLQAMRKYSPFRNGYMEPTLGQHLPTLSFPDPGLRPQNLYTLWGGSVVCMYLYQLSP 180
Brugia RPDMMSIRPTYDPYLENLKS--------------------PLIKDESDGKTLRLRFECT- 137
Haemophilus NNAILDQIEKIQQNAKSLEIK---------------------------DEQIKVLKEKS- 129
human PKGACKVPAQESQDVSGSRP---------------------------------------- 114
.

Mycobacterium -VQEAIQSTSHFEDPPEMADDYDEAWMLNTVFDYHNENAKEEVIHLVPDVNKER---GPI 213
HTLV-1 PITWPLLPHVIFCHPGQLGAFLTNVPYKRIEELLYKISLTTGALIILPEDCLPTTLFQPV 240
Brugia -VQPEEVTVKTVDNRLLVRAKHEEKTPQRAVFREYNQ------EFMLPRG------TNPE 184
Haemophilus LEAMALGAKMIKQNSELAKNPTPEAQKAFSELQVQLDKIAADGQTIEAELNKKYGISTPV 189
human --AAPLIGAPANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEE 172

Mycobacterium ELVTKVDKEGTIRLVYDG--EPTFSYKEHPKF 243
HTLV-1 PVTLTAWQNASFRSTQPSPLQALFGHLPMARL 272
Brugia LISSTLSTDGVLT------VEAPLPHLAIQH- 209
Haemophilus EATIPTINPDEIP-------EEDEEEEDENK- 213
human NVSDGSPNAGSVEQ------TPKKPGLRRRQT 198

CLUSTRAL ALIGNMENT OF P 27 PEPTIDE SEQUENCES OF HUMAN, CAT, DOG, PIG, BOVINE AND CHINESE HAMSTER
Human, cat, dog, pig, bovine and Chinese hamster are chordates and hence closely related organisms. From NCBI, p 27 peptide sequences of these organisms was obtained, which has been illustrated below:
>Human P27
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDVS GSRPAAPLIG
APANSEDTHL VDPKTDPSDS QTGLAEQCAG IRKRPATDDS STQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRRRQT

>Felca p27
MSNVRVSNGS PSLERMDARQ AEYPKPSACR NLFGPVNHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDVS GNRQAVPLIG
SQANTEDTHL VDQKTDTSDN QTGLAEQCPG IRKRPATDDS SPQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRRRQT

>Canfa p 27
MSNVRVSNGS PSLERMDARQ AEYPKPSACR NLFGPVNHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDVS GTRQAGPLLG
SQANSEDTHL VDQKTDAPDS QTGLAEQCTG IRKRPATDDS SPQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRR

>Pig p 27
MSNVRVSNGS PSLERMDARQ AEYPKPSACR NLFGPVNHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQEGQGVS GTRQAVPLIG
SQANSEDTHL VDQKTDAPDS QTGLAEQCTG IRKRPATDDS SPQNKRANRT EENVSDGSPN
SASVEQTPKK PGLRRRQT

>Bovin p 27
MSNVRVSNGS PSLERMDARQ AEYPKPSACR NLFGPVNHEE LTRDLEKHCR DMEEASQRKW
NFDFKNHKPL EGKYEWQEVE KGSLPEFYHR PPRPPKGACK VPAQEGQDAS GARPAVPLLG
SQANPEDTHL VDQKTDAPDS QTGLAEQCPG IRKRPAADDS SPQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRRRQT

>Crigr P 27
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVNHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHNPL EGRYQWQEVD KGSLPEFYYR PPRPPKGACK VPAQESQDVS GSRQAVPSIG
SQAYSEDRHL VEQMPDPTDS PAGLAEQCPG MRKRPAADDS SSQNKRANRT EENVSDGSLN
AGSVEQTPKK PGLRRHQT

The peptide sequence from fig 7, 8,9,10, 11 and 12 were entered in clustral W2 and following results were obtained:
Table 2. Scores Table obtained from Clustral W2 showing different score values

SeqA Name Len(aa) SeqB Name Len(aa) Score
=================================================
1 Human 198 2 Felca 198 93
1 Human 198 3 Canfa 195 93
1 Human 198 4 Pig 198 91
1 Human 198 5 Bovin 198 90
1 Human 198 6 Crigr 198 87
=================================================

Canfa MSNVRVSNGSPSLERMDARQAEYPKPSACRNLFGPVNHEELTRDLEKHCRDMEEASQRKW 60
Pig MSNVRVSNGSPSLERMDARQAEYPKPSACRNLFGPVNHEELTRDLEKHCRDMEEASQRKW 60
Bovin MSNVRVSNGSPSLERMDARQAEYPKPSACRNLFGPVNHEELTRDLEKHCRDMEEASQRKW 60
Felca MSNVRVSNGSPSLERMDARQAEYPKPSACRNLFGPVNHEELTRDLEKHCRDMEEASQRKW 60
Human MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW 60
Crigr MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVNHEELTRDLEKHCRDMEEASQRKW 60
**********************:*************:***********************

Canfa NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGTRQAGPLLG 120
Pig NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQEGQGVSGTRQAVPLIG 120
Bovin NFDFKNHKPLEGKYEWQEVEKGSLPEFYHRPPRPPKGACKVPAQEGQDASGARPAVPLLG 120
Felca NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGNRQAVPLIG 120
Human NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG 120
Crigr NFDFQNHNPLEGRYQWQEVDKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRQAVPSIG 120
****:**:****:*:****:********:****************.*..** * * * :*

Canfa SQANSEDTHLVDQKTDAPDSQTGLAEQCTGIRKRPATDDSSPQNKRANRTEENVSDGSPN 180
Pig SQANSEDTHLVDQKTDAPDSQTGLAEQCTGIRKRPATDDSSPQNKRANRTEENVSDGSPN 180
Bovin SQANPEDTHLVDQKTDAPDSQTGLAEQCPGIRKRPAADDSSPQNKRANRTEENVSDGSPN 180
Felca SQANTEDTHLVDQKTDTSDNQTGLAEQCPGIRKRPATDDSSPQNKRANRTEENVSDGSPN 180
Human APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN 180
Crigr SQAYSEDRHLVEQMPDPTDSPAGLAEQCPGMRKRPAADDSSSQNKRANRTEENVSDGSLN 180
: * .** ***: .*..*. :******.*:*****:****.**************** *

Canfa AGSVEQTPKKPGLRR--- 195
Pig SASVEQTPKKPGLRRRQT 198
Bovin AGSVEQTPKKPGLRRRQT 198
Felca AGSVEQTPKKPGLRRRQT 198
Human AGSVEQTPKKPGLRRRQT 198
Crigr AGSVEQTPKKPGLRRHQT 198
:.*************

CLUSTRAL ALIGNMENT OF HUMAN P 27 WILD TYPE AND VARIANT
From NCBI, following sequences were obtained:
>Wild type human P27
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDVS GSRPAAPLIG
APANSEDTHL VDPKTDPSDS QTGLAEQCAG IRKRPATDDS STQNKRANRT EENVSDGSPN
AGSVEQTPKK PGLRRRQT

>Variant human p 27
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW
NFDFQNHKPL EGKYEWQEVE KGSLPEFYYR PPRPPKGACK VPAQESQDGS GSRPAAPLIG
APANSEDTHL VDPKTDPSDS QTGLAEQCAG IRKRPATD

When the sequences from fig 14 and and 15 were entered in Clustral W2, following results were obtained:
Table 3. Scores Table obtained from Clustral W2 showing different score values
SeqA Name Len(aa) SeqB Name Len(aa) Score
=====================================================
1 variant 158 2 wild 198 99
=====================================================

variant MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW 60
wild MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW 60
************************************************************

variant NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDGSGSRPAAPLIG 120
wild NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG 120
************************************************ ***********

variant APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATD---------------------- 158
wild APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN 180
**************************************

variant ------------------
wild AGSVEQTPKKPGLRRRQT 198

DISCUSSION

Homology is the terminology used for resemblance on more than one sequences. However due to several factors like mutation, a pair of homologous genes do not possess exactly identical sequences, rather have similar sequences. Thus random changes on the original common ancestral gene lead to variation on the two sequences.

The aim of clustering is to calculate the best match of the selected sequences and to align them to reveal identities, similarities and the differences between the sequences. Additionally, evolutionary relationship between the selected sequences can be seen in phylograms.

A score value is the sum of the scoring matrix values in a pair of segment displayed. For the calculation of score value, there needs to be two sequences: sequence A and sequence B. The more the score value, the more the sequences share homology. Table 1 shows that score values of human p 27 peptide sequence with the corresponding sequences of Mycobacterium bovis, Haemophilus ducreyi, Brugia malayi, and HTLV-1, were found to be only 2, 9, 5 and 3 respectively. From evolutionary perspectives, these all organisms are distantly related to human beings because none of them are chordates. On contrast, table 2 shows that when the same human p 27 peptide sequence was aligned with the corresponding sequence of chordates like Felca (Cat), Cafna(dog), pig, bovine, Crigr(Chinese hamster) , score value were found to be as high as 93, 93, 91, 90, and 87 respectively. On phylogenic tree, chordates are more closely related with human than non chordates. That might be the cause of getting higher scores in table 2 in comparison of table 1. Similarly, table 3 shows the score value of human wild type p 27 sequence with respect to its variant sequence. As it was predicted, this score was found to be as high as 99.

Consensus symbols like “*”, “:” and “.” might be seen on clustered alignment. “*” gives the indication that amino acid residues in that column are identical. Similarly “:” and “.” are the indicators of conservation profile, where the former symbol indicates that conserved substitutions have been observed, and the latter symbol says that semi conserved substitutions have been observed(European Bioinformatics Institute, 2009).In figure 6, human p 27 sequence was aligned with corresponding sequence of non chordates. Disappearance of all consensus symbols in this figure implies that neither there is the presence identical amino acid residue nor they are conserved. In contrast, figure 13, which includes closely related organisms, shows plenty of “*”. This indicates that there are plenty of identical amino acids in human, pig, cat, dog and Chinese hamster. Some “:” and “.” present in figure 13 imply that some amino acid residues have been substituted, nevertheless , they are conserved. Clustral alignment of human p27 with its variant in figure 16 shows only “*” symbol, indicating that all the amino acid residues in the variant are exactly identical to the wild type p 27.

Gap is a space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. Figure 6 shows plenty of gaps possibly due to lack of conservation among the aligned sequence. Figure 13 is the clustral alignment of closely related species, hence does not contain any gap. Despite the high score value and presence of identical amino acid residue, gaps are present in figure 16 where the wild type p27 has been aligned to its variant . The wild type p 27 has 198 amino acids and variant bears only 157 amino acids. When these two sequences are aligned, the lack of 41 amino acid residues on the variant leads to the formation of gap in figure 16.

CONCLUSION

As the theory of evolution says, all the new species have been evolved from primitive organisms through a long process of variation and mutation. During this phenomenon, different proteins present in these organisms also must have undergone through alteration, making themselves distinct from analogous protein present in distantly related organism, however retaining similarity with the closely related organisms of phylogenic tree. Thus if we analyze from evolutionary perspectives, we see that despite retaining its functional similarity, p 27 has under gone through a profound amendments and modifications in the course of evolution. However it bears structural similarity with the closely related species and structural difference with the distantly related organism. Thus, it creates a trend of divergence if we analyze from beginning point of evolution to the current point of time.

REFERENCES

European Bioinformatics Institute, 2009. [Online]. Available from: http://www.ebi.ac.uk/Tools/blast2/index.html [Accessed 12/11/2009]

National Centerfor Biotechnology Information, 2009. [Online]. Available from: http://www.ncbi.nlm.nih.gov/ [Accessed 12 November 2009]

Polyak K et al, 1994. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals. Cell 78 (1): 59-66.

Chen J, Amos CI, Merriman KW, Wei Q, Sen S, Killary AM, Frazier ML, 2009.Genetic Variants of p21 and p27 and Pancreatic Cancer Risk in Non-Hispanic Whites: A Case-Control Study: Pub med

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