International Journal of Bioprocess and Biotechnological Advancements (ISSN:2380-0259)
Commentary
Fc Receptor Genes in Asterias Rubens (Echinodermata) when Compared to Mammals
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The Fc receptor gene of Asterias rubens (Echinodermata, Invertebrates) present at least 33 % identities with 7 Fc receptor Mammal genes by using the following method of Compositional matrix adjust. The e-values are highly significative.
Keywords: Asterias Rubens, Invertebrates, Fc receptor gene, Mammal Fc genes
INTRODUCTION
In 2016, we have isolated the Asterias rubens Fc receptor gene [1]. It was the first time such discovery, in Invertebrates was performed.
In the present work we analyzed the identities between this gene and mammal Fc receptor genes by the use of Compositional matrix adjust [2] and blasts against mammal’s protein.
The A. rubens starting material (DNA sequence in 5’-3’) is the following:
TCCATTAGGGCAATGAGTGGGACTGCGCGGCTTGGCACAGATCATCCCTTTTCTATCACGACACCTCGAGTCTTTCCACTTGCCGTTGCTAATCTGTAATGCCACACAGTTATTCTCCAATGATTCGACTCCAGACAGCTCAGTTTGCTCTTCTTCGATGAAGTTCGTGTAGTTGACGGGGGAATCGTTTGACCATTTCCAATCGCTTTCGTTGTGTGTATCATGGAGCCCGATCCACACGTCCCTGTCAATTAGGTCGGTAAGAAAATCATTAATTTCTTGGTCAGTGATGGCGACCAGCCTAGCGCCGTCGTATTTAGTGCACTTCTGTTCAGCATCGACCCAGCGTGCTACATCGTCTGGAATCCAGAAGCATTCATCACGGAAGAGATGGCCGTTGTTTAGGCAGTACTGTGGTTGACCACGTACTGTTTGAAGAAGATGAGCTGACCCAATAACCATCATCATCACGAATGGAATCATTGTGAATTTGTTTGAGATACGTCCGATACGTCCGTCCGTAGATGAAAAAACTGCCGAAGTCTCTCACATAATTCCACCAGGCATTGTTGATGCCTTGCTGCTCTATGGTTGATGCTTGGTGGCAGTCCACGAAAGAATGTGCAGTTAGGGAAAGTCCAGCTTGTATATCTC
RESULTS
7 Fc mammal sequences which present high identities with ours [1] are given now with their characteristics:
- Predicted: low affinity immunoglobulin epsilon Fc receptor [Dipodomys ordii]
Sequence ID: XP_012889053.1 Length: 306
Range 1: 172 to 296
Score: 77.8 bits (190), Expect: 7e-13,
Method: Compositional matrix adjust.,
Identities: 43/131(33%), Positives: 69/131(52%), Gaps: 13/131(9%)
Query 387 FRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDRDVWIGLHDTHNE 208
F+ +C++ + RW+ A C+ +G RLV+I QE DFL+ + +D WIGL D E
Subject 172 FQQKCYYFGEGTKRWLQARFACSDLEG-RLVSIHSQEEQDFLSKHVSKDAWIGLQDLDVE 230
Query 207 SDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRDR-------K 49
++ W + SPV+Y+N+++ E E +CV ++ S G W D+ CR + +
Subject 231 GEFVWMDGSPVSYSNWLQGEPNNAGSDE----DCVMMRGS-GHWNDAFCRSQLDTWVCER 285
Query 48 GMICAKPRSPT 16…….C P PT
Subject 286 LATCGPPALPT 296
- Low affinity immunoglobulin epsilon Fc receptor [Dipodomys spectabilis]
Sequence ID: XP_042549638.1 Length: 306
>low affinity immunoglobulin epsilon Fc receptor [Dipodomys spectabilis]
Sequence ID: XP_042549639.1 Length: 306
>low affinity immunoglobulin epsilon Fc receptor [Dipodomys spectabilis]
Sequence ID: XP_042549640.1 Length: 306
Range 1: 172 to 296
Score: 77.8 bits (190), Expect: 8e-13,
Method: Compositional matrix adjust.,
Identities: 43/131(33%), Positives: 69/131(52%), Gaps: 13/131(9%)
Query 387 FRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDRDVWIGLHDTHNE 208
F+ +C++ + RW+ A C+ +G RLV+I QE DFL+ + +D WIGL D E
Sbjct 172 FQQKCYYFGEGTKRWLQARFACSDLEG-RLVSIHSQEEQDFLSKHVSKDAWIGLQDLDVE 230
Query 207 SDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRDR-------K 49
++ W + SPV+Y+N+++ E E +CV ++ S G W D+ CR + +
Subject 231 GEFVWMDGSPVSYSNWLQGEPNNAGSDE----DCVMMRGS-GHWNDAFCRSQLDTWVCER 285
Query 48 GMICAKPRSPT 16
C P PT
Subject 286 LATCGPPA
- Low affinity immunoglobulin epsilon Fc receptor [Microtus ochrogaster]
Sequence ID: XP_005371819.1 Length: 172
Range 1: 27 to 147
Score: 72.0 bits (175), Expect: 1e-11,
Method: Compositional matrix adjust.,
Identities: 42/127(33%), Positives: 67/127(52%), Gaps: 7/127(5%)
Query 408 CLNNGHLFRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDRDVWIG 229
C N F+ +C++ +D RW+ A C+ G RLV+I QE +FL ++D WIG
Subject 27 CPKNWLHFQQKCYYFGNDSKRWIQARFTCSDLKG-RLVSIHSQEEQNFLMKHTNKDSWIG 85
Query 228 LHDTHNESDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRD-R 52
L D + E ++ W + SPV Y+N+ E E +CV ++ S G+W D+ C
Subject 86 LRDLNVEGEFIWMDGSPVGYSNWSPGEPNNAGQGE----DCVMMRGS-GQWNDAFCHSFL 140
Query 51 KGMICAK 31
+G +C +
Subject 141 EGWVCEQ 147
- Low affinity immunoglobulin epsilon Fc receptor-like, partial [Nannospalax galili]
Sequence ID: XP_008853602.1 Length: 154
Range 1: 11 to 122
Score: 71.2 bits (173), Expect: 2e-11,
Method: Compositional matrix adjust.,
Identities: 42/118(36%), Positives: 61/118(51%), Gaps: 6/118(5%)
Query 408 CLNNGHLFRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDRDVWIG 229
C N F+ +C++ +W+ A+ C+ G +LV+I QE DFLT I D WIG
Subject 11 CPKNWLNFQQKCYYFGKGSKQWIQAKFTCSNLKG-QLVSIHSQEEQDFLTKHIKEDSWIG 69
Query 228 LHDTHNESDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRD 55
L D E ++ W +DSPV Y+N+ E E +CV + S G+W D+ CR
Sbjct 70 LRDLFTEGEFVWMDDSPVGYSNWNPGEPNNGGQGE----DCVMMWGS-GQWNDAFCRS 122
- Fc fragment of IgE receptor II [Rhinolophus ferrumequinum]
Sequence ID: KAF6306204.1 Length: 290
Range 1: 169 to 284
Score: 73.2 bits (178), Expect: 3e-11,
Method: Compositional matrix adjust.,
Identities: 42/119(35%), Positives: 69/119(57%), Gaps: 5/119(4%)
Query 387 FRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDR-DVWIGLHDTHN 211
F+ +C++ + RW+ A C+K G RLV+I QE DFL I R WIGL D +
Subject 169 FQRKCYYFGEGAKRWIQARLACSKLQG-RLVSIHSQEEQDFLAKSIHRRGSWIGLRDLNI 227
Query 210 ESDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRDR-KGMIC 37
E D+ W +++P++Y+N+ E + G L +CV + +S+G+W D+ C ++ G +C
Subject 228 EGDFVWMDENPLDYSNWRPGEPND-GGERGLGEDCVMM-LSSGQWNDAFCGNQLDGWVC 284
- Low affinity immunoglobulin epsilon Fc receptor [Rhinolophus ferrumequinum]
Sequence ID: XP_032990569.1 Length: 305
Range 1: 184 to 299
Score: 72.8 bits (177), Expect: 4e-11,
Method: Compositional matrix adjust.,
Identities: 42/119(35%), Positives: 69/119(57%), Gaps: 5/119(4%)
Query 387 FRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDR-DVWIGLHDTHN 211
F+ +C++ + RW+ A C+K G RLV+I QE DFL I R WIGL D +
Subject 184 FQRKCYYFGEGAKRWIQARLACSKLQG-RLVSIHSQEEQDFLAKSIHRRGSWIGLRDLNI 242
Query 210 ESDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRDR-KGMIC 37
E D+ W +++P++Y+N+ E + G L +CV + +S+G+W D+ C ++ G +C
Sbjct 243 EGDFVWMDENPLDYSNWRPGEPND-GGERGLGEDCVMM-LSSGQWNDAFCGNQLDGWVC 299
- PREDICTED: low affinity immunoglobulin epsilon Fc receptor isoform X1 [Hipposideros armiger]
Sequence ID: XP_019523150.1 Length: 385
Range 1: 267 to 381
Score: 73.2 bits (178), Expect: 5e-11,
Method: Compositional matrix adjust.,
Identities: 43/121(36%), Positives: 70/121(57%), Gaps: 8/121(6%)
Query 387 FRDECFWIPDDVARWVDAEQKCTKYDGARLVAITDQEINDFLTDLIDR-DVWIGLHDTHN 211
F+ +C++ + RW+ A C+K G RLV+I QE DFL I+R + WIGL D +
Subject 267 FQRKCYYFGEGAKRWIQARLACSKLQG-RLVSIHSQEEQDFLVKHINRKESWIGLRDLNI 325
Query 210 ESDWKWSNDSPVNYTNFIEEEQTELSGVESLENNCVALQISNGKWKDSRCRD-RKGMICA 34
E ++ W +++PVNY+N+ E +G E +CV + +S+G+W D+ C G +C
Subject 326 EGNFVWMDENPVNYSNWRPGEPN--NGGEG--EDCV-MMLSSGQWNDAFCNSLLNGWVCE 380
Query 33 K 31
+
Subject 381 R 381
CONCLUSION
The sea star A. rubens Fc receptor gene shows identities from 33 % To 36 % with 7 Fc receptor mammal genes. We notice just one identity with mammal IgE out of 7.
Mainly, 3 classes of Echinodermata out of 5 present the Fc receptor gene [3,4]: the Asterids, the Ophuirids and the Crinoids. 2 classes have not: the Echinids and the Holothurids. We recall also that the Ophuirids, with the Ophiocomina nigra as a model of study, are the most evolved of Echinodermata, since the IgK O.nigra shows high similitudes with the Human IgK.
- Leclerc M, Kresdorn N (2016) Evidence of low affinity immunoglobulin epsilon Fc receptor gene in an invertebrate: The sea star Asterias rubens. Clin Res Trials 2(2): 152-153.
- Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J 272(20): 5101-5109.
- Leclerc M (2018) Evidence of Fc Receptor Gene in an Ophuirid: Ophiocomina Nigra. Int J Biotech Bioeng 4(3): 35-36.
- Leclerc M, Letourneur F, Davoult D, Jolly A, de la Grange P (2018) Evidence of immune genes in the crinoïd: Antedon bifida evidence of bifida Igkappa gene and a FC receptor one. J Appl Biotechnol Bioeng 5(5): 303-304.
