The ABC transporter gene family of <it>Daphnia pulex</it>

<p>Abstract</p> <p>Background</p> <p>The large gene superfamily of ABC (ATP-binding cassette) transporters encodes membrane proteins involved in trafficking processes across biological membranes and further essential cell biological functions. ABC transporters are evolu...

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Main Authors: Cunningham Phil, Sturm Armin, Dean Michael
Format: Article
Language:English
Published: BMC 2009-04-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/10/170
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author Cunningham Phil
Sturm Armin
Dean Michael
author_facet Cunningham Phil
Sturm Armin
Dean Michael
author_sort Cunningham Phil
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>The large gene superfamily of ABC (ATP-binding cassette) transporters encodes membrane proteins involved in trafficking processes across biological membranes and further essential cell biological functions. ABC transporters are evolutionary ancient and involved in the biochemical defence against toxicants. We report here a genome-wide survey of ABC proteins of <it>Daphnia pulex</it>, providing for the first time information on ABC proteins in crustacea, a primarily aquatic arthropod subphylum of high ecological and economical importance.</p> <p>Results</p> <p>We identified 64 ABC proteins in the <it>Daphnia </it>genome, which possesses members of all current ABC subfamilies A to H. To unravel phylogenetic relationships, ABC proteins of <it>Daphnia </it>were compared to those from yeast, worm, fruit fly and human. A high conservation of <it>Daphnia </it>of ABC transporters was observed for proteins involved in fundamental cellular processes, including the mitochondrial half transporters of the ABCB subfamily, which function in iron metabolism and transport of Fe/S protein precursors, and the members of subfamilies ABCD, ABCE and ABCF, which have roles in very long chain fatty acid transport, initiation of gene transcription and protein translation, respectively. A number of <it>Daphnia </it>proteins showed one-to-one orthologous relationships to <it>Drosophila </it>ABC proteins including the sulfonyl urea receptor (<it>SUR</it>), the ecdysone transporter <it>ET23</it>, and the eye pigment precursor transporter <it>scarlet</it>. As the fruit fly, <it>Daphnia </it>lacked homologues to the TAP protein, which plays a role in antigene processing, and the cystic fibrosis transmembrane conductance regulator (CFTR), which functions as a chloride channel. <it>Daphnia </it>showed two proteins homologous to MDR (multidrug resistance) P-glycoproteins (ABCB subfamily) and six proteins homologous to MRPs (multidrug resistance-associated proteins) (ABCC subfamily). However, lineage specific gene duplications in the ABCB and ABCC subfamilies complicated the inference of function. A particularly high number of gene duplications were observed in the ABCG and ABCH subfamilies, which have 23 and 15 members, respectively.</p> <p>Conclusion</p> <p>The <it>in silico </it>characterisation of ABC transporters in the <it>Daphnia pulex </it>genome revealed that the complement of ABC transporters is as complex in crustaceans as that other metazoans. Not surprisingly, among currently available genomes, <it>Daphnia </it>ABC transporters most closely resemble those of the fruit fly, another arthropod.</p>
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spelling doaj.art-b288c08a239e4638b364d0c2e7b7e47f2022-12-22T02:59:56ZengBMCBMC Genomics1471-21642009-04-0110117010.1186/1471-2164-10-170The ABC transporter gene family of <it>Daphnia pulex</it>Cunningham PhilSturm ArminDean Michael<p>Abstract</p> <p>Background</p> <p>The large gene superfamily of ABC (ATP-binding cassette) transporters encodes membrane proteins involved in trafficking processes across biological membranes and further essential cell biological functions. ABC transporters are evolutionary ancient and involved in the biochemical defence against toxicants. We report here a genome-wide survey of ABC proteins of <it>Daphnia pulex</it>, providing for the first time information on ABC proteins in crustacea, a primarily aquatic arthropod subphylum of high ecological and economical importance.</p> <p>Results</p> <p>We identified 64 ABC proteins in the <it>Daphnia </it>genome, which possesses members of all current ABC subfamilies A to H. To unravel phylogenetic relationships, ABC proteins of <it>Daphnia </it>were compared to those from yeast, worm, fruit fly and human. A high conservation of <it>Daphnia </it>of ABC transporters was observed for proteins involved in fundamental cellular processes, including the mitochondrial half transporters of the ABCB subfamily, which function in iron metabolism and transport of Fe/S protein precursors, and the members of subfamilies ABCD, ABCE and ABCF, which have roles in very long chain fatty acid transport, initiation of gene transcription and protein translation, respectively. A number of <it>Daphnia </it>proteins showed one-to-one orthologous relationships to <it>Drosophila </it>ABC proteins including the sulfonyl urea receptor (<it>SUR</it>), the ecdysone transporter <it>ET23</it>, and the eye pigment precursor transporter <it>scarlet</it>. As the fruit fly, <it>Daphnia </it>lacked homologues to the TAP protein, which plays a role in antigene processing, and the cystic fibrosis transmembrane conductance regulator (CFTR), which functions as a chloride channel. <it>Daphnia </it>showed two proteins homologous to MDR (multidrug resistance) P-glycoproteins (ABCB subfamily) and six proteins homologous to MRPs (multidrug resistance-associated proteins) (ABCC subfamily). However, lineage specific gene duplications in the ABCB and ABCC subfamilies complicated the inference of function. A particularly high number of gene duplications were observed in the ABCG and ABCH subfamilies, which have 23 and 15 members, respectively.</p> <p>Conclusion</p> <p>The <it>in silico </it>characterisation of ABC transporters in the <it>Daphnia pulex </it>genome revealed that the complement of ABC transporters is as complex in crustaceans as that other metazoans. Not surprisingly, among currently available genomes, <it>Daphnia </it>ABC transporters most closely resemble those of the fruit fly, another arthropod.</p>http://www.biomedcentral.com/1471-2164/10/170
spellingShingle Cunningham Phil
Sturm Armin
Dean Michael
The ABC transporter gene family of <it>Daphnia pulex</it>
BMC Genomics
title The ABC transporter gene family of <it>Daphnia pulex</it>
title_full The ABC transporter gene family of <it>Daphnia pulex</it>
title_fullStr The ABC transporter gene family of <it>Daphnia pulex</it>
title_full_unstemmed The ABC transporter gene family of <it>Daphnia pulex</it>
title_short The ABC transporter gene family of <it>Daphnia pulex</it>
title_sort abc transporter gene family of it daphnia pulex it
url http://www.biomedcentral.com/1471-2164/10/170
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