The ABC transporter gene family of Daphnia pulex

Sturm, Armin; Cunningham, Phil; Dean, Michael

doi:10.1186/1471-2164-10-170

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; DOE/OSTI
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.

View Accepted Manuscript (DOE)

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

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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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
Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey Ren, Jianfeng; Chung-Davidson, Yu-Wen; Yeh, Chu-Yin BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1677-z	journal	June 2015
Characterization and expression profiling of ATP-binding cassette transporter genes in the diamondback moth, Plutella xylostella (L.) Qi, Weiping; Ma, Xiaoli; He, Weiyi BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3096-1	journal	September 2016
Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family Adedipe, Folukemi; Grubbs, Nathaniel; Coates, Brad BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6218-8	journal	November 2019
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
Genome-wide survey of cytochrome P450 genes in the salmon louse Lepeophtheirus salmonis (Krøyer, 1837) Humble, Joseph L.; Carmona-Antoñanzas, Greta; McNair, Carol M. Parasites & Vectors, Vol. 12, Issue 1 https://doi.org/10.1186/s13071-019-3808-x	journal	November 2019
Analysis of the Olive Fruit Fly Bactrocera oleae Transcriptome and Phylogenetic Classification of the Major Detoxification Gene Families Pavlidi, Nena; Dermauw, Wannes; Rombauts, Stephane PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0066533	journal	June 2013
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
Generation of white-eyed Daphnia magna mutants lacking scarlet function Ismail, Nur Izzatur Binti; Kato, Yasuhiko; Matsuura, Tomoaki PLOS ONE, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pone.0205609	journal	November 2018
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
Insect ATP-Binding Cassette (ABC) Transporters: Roles in Xenobiotic Detoxification and Bt Insecticidal Activity Wu, Chao; Chakrabarty, Swapan; Jin, Minghui International Journal of Molecular Sciences, Vol. 20, Issue 11 https://doi.org/10.3390/ijms20112829	journal	June 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
Identification of a putatively multixenobiotic resistance related Abcb1 transporter in amphipod species endemic to the highly pristine Lake Baikal Pavlichenko, Vasiliy V.; Protopopova, Marina V.; Timofeyev, Maxim Environmental Science and Pollution Research, Vol. 22, Issue 7 https://doi.org/10.1007/s11356-014-3758-y	journal	November 2014
Generation of white-eyed Daphnia magna mutants lacking scarlet function Binti Ismail, Nur Izzatur; Kato, Yasuhiko; Matsuura, Tomoaki https://doi.org/10.1101/313395	posted_content	May 2018
Rapid evolutionary loss of metal resistance revealed by hatching decades-old eggs: RAPID LOSS OF LEAD RESISTANCE Turko, Patrick; Sigg, Laura; Hollender, Juliane Evolution, Vol. 70, Issue 2 https://doi.org/10.1111/evo.12859	journal	February 2016
Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress: Auxin transporter gene families in Sorghum bicolor Shen, ChenJia; Bai, YouHuang; Wang, SuiKang FEBS Journal, Vol. 277, Issue 14 https://doi.org/10.1111/j.1742-4658.2010.07706.x	journal	June 2010
The water flea Daphnia - a 'new' model system for ecology and evolution? Stollewerk, Angelika Journal of Biology, Vol. 9, Issue 2 https://doi.org/10.1186/jbiol212	journal	January 2010
Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci Tian, Lixia; Song, Tianxue; He, Rongjun BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3706-6	journal	April 2017
Phylogenetic analysis of the ATP-binding cassette proteins suggests a new ABC protein subfamily J in Aedes aegypti (Diptera: Culicidae) Figueira-Mansur, Janaina; Schrago, Carlos G.; Salles, Tiago S. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-06873-8	journal	July 2020
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/v1	posted_content	November 2019
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
Diversity and evolution of ABC proteins in basidiomycetes Kovalchuk, Andriy; Lee, Yong-Hwan; Asiegbu, Fred O. Mycologia, Vol. 105, Issue 6 https://doi.org/10.3852/13-001	journal	November 2013

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