The ABC transporter gene family of Daphnia pulex

Sturm, Armin; Cunningham, Phil; Dean, Michael

doi:10.1186/1471-2164-10-170

Title: The ABC transporter gene family of Daphnia pulex

Journal Article · Thu Jan 01 00:00:00 EST 2009 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-10-170· OSTI ID:1626392

Sturm, Armin ^[1]; Cunningham, Phil ^[2]; Dean, Michael ^[3]

Univ. of Stirling (United Kingdom). Inst. of Aquaculture
King's College, London (United Kingdom). Dept. of Biochemistry
National Cancer Institute, Bethesda, MD (United States). Lab. of Genomic Diversity

Background: 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 Daphnia pulex, providing for the first time information on ABC proteins in crustacea, a primarily aquatic arthropod subphylum of high ecological and economical importance. Results: We identified 64 ABC proteins in the Daphnia genome, which possesses members of all current ABC subfamilies A to H. To unravel phylogenetic relationships, ABC proteins of Daphnia were compared to those from yeast, worm, fruit fly and human. A high conservation of Daphnia 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 Daphnia proteins showed one-to-one orthologous relationships to Drosophila ABC proteins including the sulfonyl urea receptor (SUR), the ecdysone transporter ET23, and the eye pigment precursor transporter scarlet. As the fruit fly, Daphnia 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. Daphnia 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. Conclusion: The in silico characterisation of ABC transporters in the Daphnia pulex genome revealed that the complement of ABC transporters is as complex in crustaceans as that other metazoans. Not surprisingly, among currently available genomes, Daphnia ABC transporters most closely resemble those of the fruit fly, another arthropod.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, San Diego, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; W-7405-ENG-48

OSTI ID:: 1626392

Journal Information:: BMC Genomics, Vol. 10, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family Adedipe, Folukemi; Grubbs, Nathaniel; Coates, Brad BMC Genomics https://doi.org/10.21203/rs.2.9611/v2	posted_content	November 2019
The novel ABC transporter ABCH1 is a potential target for RNAi-based insect pest control and resistance management Guo, Zhaojiang; Kang, Shi; Zhu, Xun Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep13728	journal	September 2015
Actin polymerization controls the activation of multidrug efflux at fertilization by translocation and fine-scale positioning of ABCB1 on microvilli Whalen, Kristen; Reitzel, Adam M.; Hamdoun, Amro Molecular Biology of the Cell, Vol. 23, Issue 18 https://doi.org/10.1091/mbc.e12-06-0438	journal	September 2012
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex Rappoport, Nadav; Linial, Michal BMC Bioinformatics, Vol. 14, Issue S3 https://doi.org/10.1186/1471-2105-14-s3-s11	journal	February 2013
Phylogenetic analysis of fungal ABC transporters Kovalchuk, Andriy; Driessen, Arnold JM BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-177	journal	January 2010
A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae Dermauw, Wannes; Osborne, Edward; Clark, Richard M. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-317	journal	January 2013
Functional analysis of the ATP-binding cassette (ABC) transporter gene family of Tribolium castaneum Broehan, Gunnar; Kroeger, Tobias; Lorenzen, Marcé BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-6	journal	January 2013
Genome-wide identification of whole ATP-binding cassette (ABC) transporters in the intertidal copepod Tigriopus japonicus Jeong, Chang-Bum; Kim, Bo-Mi; Lee, Jae-Seong BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-651	journal	August 2014
Deciphering the genetic basis of microcystin tolerance Schwarzenberger, Anke; Sadler, Thomas; Motameny, Susanne BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-776	journal	January 2014
Transcriptomic insights on the ABC transporter gene family in the salmon louse Caligus rogercresseyi Valenzuela-Muñoz, Valentina; Sturm, Armin; Gallardo-Escárate, Cristian Parasites & Vectors, Vol. 8, Issue 1 https://doi.org/10.1186/s13071-015-0801-x	journal	April 2015
A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis) Carmona-Antoñanzas, Greta; Carmichael, Stephen N.; Heumann, Jan PLOS ONE, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pone.0137394	journal	September 2015
Molecular Cloning and Characterization of a P-Glycoprotein from the Diamondback Moth, Plutella xylostella (Lepidoptera: Plutellidae) Tian, Lixia; Yang, Jiaqiang; Hou, Wenjie International Journal of Molecular Sciences, Vol. 14, Issue 11 https://doi.org/10.3390/ijms141122891	journal	November 2013
Evidence for the Induction of Key Components of the NOTCH Signaling Pathway via Deltamethrin and Azamethiphos Treatment in the Sea Louse Caligus rogercresseyi Boltaña, Sebastian; Chávez-Mardones, Jaqueline; Valenzuela-Muñoz, Valentina International Journal of Molecular Sciences, Vol. 17, Issue 5 https://doi.org/10.3390/ijms17050304	journal	May 2016
ATP-Binding Cassette (ABC) Transporter Genes Involved in Pyrethroid Resistance in the Malaria Vector Anopheles sinensis: Genome-Wide Identification, Characteristics, Phylogenetics, and Expression Profile He, Qiyi; Yan, Zhentian; Si, Fengling International Journal of Molecular Sciences, Vol. 20, Issue 6 https://doi.org/10.3390/ijms20061409	journal	March 2019
Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies Rao, R. Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd Bioinformatics and Biology Insights, Vol. 4 https://doi.org/10.4137/bbi.s4337	journal	January 2010

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