ATP-binding Cassette Gene Family Research Articles

Genome-wide identification, phylogeny, evolutionary expansion, and expression analyses of ABC gene family in Castanea mollissima under temperature stress.

The ATP-binding cassette (ABC) gene family comprises some of the most critical transporter proteins in plants, playing vital roles in maintaining cellular homeostasis and adapting to environmental changes. While ABC transporters have been extensively characterized in various plant species, their profile in C. mollissima remains less understood. In this study, 164 ABC genes were identified and characterized within the C. mollissima genome, and subsequently classified into eight subfamilies. Collinear analysis suggested that dispersed duplication was the primary mechanism driving the expansion of the CmABC gene family. The study also examined morphological and physiological changes in C. mollissima under temperature stress, highlighting significant decreases in photosynthetic indicators and SOD enzyme activity, while other indicators varied. Transcriptome analysis revealed distinct expression patterns of various CmABC genes under temperature stress, identifying CmABCG29c and CmABCB11e as key candidates for responding to temperature stress. This was based on their expression patterns, correlation with physiological indicators, and WGCNA analysis. The expression levels of CmABC genes measured in RT-qPCR experiments were consistent with those observed in RNA-seq analysis. This research provides a theoretical foundation for understanding the physiological and gene expression responses of C. mollissima to temperature stress.

Genome-Wide Identification of the ABC Gene Family in Rosaceae and Its Evolution and Expression in Response to Valsa Canker

The ATP-binding cassette (ABC) transporter family plays a critical role in plant growth, development, and disease resistance. However, the evolution and functional characteristics of the ABC gene family in Rosaceae species have not been fully studied. In this study, we performed the first whole-genome identification, as well as an evolutionary analysis and comparative analysis of ABC genes in Rosaceae plants. We identified 3037 ABC genes in 20 plant species, classifying them into eight subfamilies. Comparative analysis revealed significant variations in family size and expansion patterns among species, suggesting adaptive evolution. Tandem duplication (TD: where genes are duplicated in sequence) and whole-genome duplication (WGD: duplication of the entire genome) were identified as the primary drivers of ABC family expansion. In pears, gene pairs produced by WGD underwent purifying selection. Gene ontology (GO) enrichment analysis indicated the involvement of ABC proteins in transmembrane transport and signal transduction pathways. Under Valsa pyri infection, most ABC genes were upregulated in the early stages, highlighting the role of ABCG genes in pathogen response. A weighted gene co-expression network analysis (WGCNA) identified five key ABCG genes potentially involved in pathogen resistance regulation. Our findings provide insights into the evolutionary adaptability of the ABC gene family and their potential applications in plant disease defense.

Genome wide identification and expression profiling of ATP binding cassette (ABC) transporters gene family in lentil (Lens culinaris Medikus) under aluminium stress condition

Adenosine triphosphate-binding cassette transporters (ABC transporters) are involved in regulating plant growth, development and tolerance to environmental stresses. In this study, a total of 138 ABC transporter genes were identified in the lentil genome that were classified into eight subfamilies. Four lentil ABC transporters from subfamily B and I were clustered together with the previously characterized ABC transporter proteins related to aluminium (Al) detoxification. Lentil ABC transporter genes were distributed across the chromosomes. Tandem duplication was the main driving force for expansion of the ABC gene family. Collinearity of lentil with soybean indicated that ABC gene family is closely linked to Glycine max. ABC genes in the same subfamily showed similar gene structure and conserved motifs. The ABC promoter regions harboured a large number of plant hormones and multiple stress responsive cis-regulatory elements. The qRT-PCR showed that ABC genes had varied expression in roots of lentil at different time points under Al stress. This is the first report on genome wide identification and expression analyses of genes encoding ABC transporter genes in lentil which has provided in-depth insight for future research on evolution and elucidation of molecular mechanisms for aluminium tolerance.

Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri)

BackgroundATP-binding cassette (ABC) transporter proteins constitute a plant gene superfamily crucial for growth, development, and responses to environmental stresses. Despite their identification in various plants like maize, rice, and Arabidopsis, little is known about the information on ABC transporters in pear. To investigate the functions of ABC transporters in pear development and abiotic stress response, we conducted an extensive analysis of ABC gene family in the pear genome.ResultsIn this study, 177 ABC transporter genes were successfully identified in the pear genome, classified into seven subfamilies: 8 ABCAs, 40 ABCBs, 24 ABCCs, 8 ABCDs, 9 ABCEs, 8 ABCFs, and 80 ABCGs. Ten motifs were common among all ABC transporter proteins, while distinct motif structures were observed for each subfamily. Distribution analysis revealed 85 PbrABC transporter genes across 17 chromosomes, driven primarily by WGD and dispersed duplication. Cis-regulatory element analysis of PbrABC promoters indicated associations with phytohormones and stress responses. Tissue-specific expression profiles demonstrated varied expression levels across tissues, suggesting diverse functions in development. Furthermore, several PbrABC genes responded to abiotic stresses, with 82 genes sensitive to salt stress, including 40 upregulated and 23 downregulated genes. Additionally, 91 genes were responsive to drought stress, with 22 upregulated and 36 downregulated genes. These findings highlight the pivotal role of PbrABC genes in abiotic stress responses.ConclusionThis study provides evolutionary insights into PbrABC transporter genes, establishing a foundation for future research on their functions in pear. The identified motifs, distribution patterns, and stress-responsive expressions contribute to understanding the regulatory mechanisms of ABC transporters in pear. The observed tissue-specific expression profiles suggest diverse roles in developmental processes. Notably, the significant responses to salt and drought stress emphasize the importance of PbrABC genes in mediating adaptive responses. Overall, our study advances the understanding of PbrABC transporter genes in pear, opening avenues for further investigations in plant molecular biology and stress physiology.

Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress

ABC (ATP-binding cassette) transporter proteins are one of the most extensive protein families known to date and are ubiquitously found in animals, plants, and microorganisms. ABCs have a variety of functions, such as plant tissue development regulation, hormone transport, and biotic and abiotic stress resistance. However, the gene characterization and function of the ABC gene family in almond (Prunus dulcis) have not been thoroughly studied. In this study, we identified 117 PdABC genes using the whole genome of ‘Wanfeng’ almond obtained by sequencing and explored their protein characterization. The PdABC family members were classified into eight subfamilies. The members of the same subfamily had conserved motifs but poorly conserved numbers of exons and introns and were unevenly distributed among the eight subfamilies and on the eight chromosomes. Expression patterns showed that PdABC family members were significantly differentially expressed during almond development, dormant freezing stress, and salt stress. We found that PdABC59 and PdABC77 had extremely high expression levels in pollen. PdABC63 and PdABC64 had high expression levels during almond petal development and multiple stages of flower development. PdABC98 was highly expressed in annual dormant branches after six temperature-freezing stress treatments. PdABC29, PdABC69, and PdABC98 were highly expressed under different concentrations of salt stress. This study preliminarily investigated the expression characteristics of ABC genes in different tissues of almond during flower development, freezing stress and salt stress, and the results will provide a reference for further in-depth research and breeding of almond in the future.

Genome-wide identification and characterization of ABC transporter superfamily in the legume Cajanus cajan.

Plant ATP-binding cassette (ABC) protein family is the largest multifunctional highly conserved protein superfamily that transports diverse substrates across biological membranes by the hydrolysis of ATP and is also the part of the several other biological processes like cellular detoxification, growth and development, stress biology, and signaling processes. In the agriculturally important legume crop Cajanus cajan, a genome-wide identification and characterization of the ABC gene family was carried out. A total of 159 ABC genes were identified that belong to eight canonical classes CcABCA to CcABCG and CcABCI based on the phylogenetic analysis. The number of genes was highest in CcABCG followed by CcABCC and CcABCB class. A total of 85 CcABC genes were found on 11 chromosomes and 74 were found on scaffold. Tandem duplication was the major driver of CcABC gene family expansion. The dN/dS ratio revealed the purifying selection. The phylogenetic analysis revealed class-specific eight superclades which reflect their functional importance. The largest clade was found to be CcABCG which reflects their functional significance. CcABC proteins were mainly basic in nature and found to be localized in the plasma membrane. The secondary structure prediction revealed the dominance of α-helix. The canonical transmembrane and nucleotide binding domain, signature motif LSSGQ, Walker A, Walker B region, and Q loop were also identified. A class-specific exon-intron pattern was also observed. In addition to core elements, different cis-acting regulatory elements like stress, hormone, and cellular responsive were also identified. Expression profiling of CcABC genes at various developmental stages of different anatomical tissues was performed and it was noticed that CcABCF3, CcABCF4, CcABCF5, CcABCG66, and CcABCI3 had the highest expression. The results of the current study endow us with the further functional analysis of Cajanus ABC in the future.

Genome-wide identification and expression pattern profiling of the ATP-binding cassette gene family in tea plant (Camelliasinensis)

The ATP-binding cassette (ABC) gene family is one of the largest and oldest protein families, consisting of ATP-driven transporters facilitating substrate transportation across cell membranes. However, little is known about the evolution and biological function of the ABC gene family in tea plants. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in Camellia sinensis. Our analysis of 170 ABC genes revealed that CsABCs were unevenly distributed across 15 chromosomes, with an amino acid length ranging from 188 to 2489 aa, molecular weight ranging from 20.29 to 277.34 kDa, and an isoelectric point ranging from 4.89 to 10.63. Phylogenetic analysis showed that CsABCs were divided into eight subfamilies, among which the ABCG subfamily was the most abundant. Furthermore, the subcellular localization of CsABCs indicated that they were present in various organelles. Collinearity analysis between the tea plant and Arabidopsis thaliana genomes revealed that the CsABC genes were homologous to the AtABC genes. Large gene fragment duplication analysis identified ten gene pairs as tandem repeats, and interaction network analysis demonstrated that CsABCs interacted with various types of target genes, with protein interactions also occurring within the family. Tissue expression analysis indicated that CsABCs were highly expressed in roots, stems, and leaves and were easily induced by drought and cold stress. Moreover, qRT-PCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results. Identifying ABC genes in tea plants lays a foundation for the classification and functional analysis of ABC family genes, which can facilitate molecular breeding and the development of new tea varieties.

Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’

ATP-binding cassette (ABC) transporters are a large class of superfamily involved in a variety of biological processes with multiple functions, including phytohormone transport, heavy metal ion detoxification, and so on. Anthocyanin pigmentation in grapes is a commercially important feature of this superfamily. To elucidate the mechanisms of the VvABC gene at different stages in grape berries, we analyzed and characterized the ABC family in ‘ZhongShan-HongYu’ (ZS-HY) berries using RNA-seq analysis. In this study, a total of 146 VvABC genes were identified by comprehensive bioinformatics analysis, which outlined their gene structure, chromosomal location, conserved domains, phylogenetic relationships, and collinearity analysis. The VvABC family could be divided into eight subfamilies based on the phylogenetic analysis. Fifty-eight VvABC genes were identified from the RNA-seq data, of which 31 belong to the ABCG subfamily, 15 belong to the ABCC subfamily, 8 belong to the ABCB subfamily, 2 belong to the ABCF subfamily, and only 1 belongs to each of the ABCA and ABCD subfamilies. We used qRT-PCR to detect the expression of VvABC genes in different organs and found that it changed significantly in different organs. Phylogenetic analysis showed that genes involved in anthocyanin transport in other species were closely related to members of the ABCC subfamily. Subsequently, analysis of the promoter elements and the protein interactions of the VvABCC genes using RNA-seq was performed. This study has improved our understanding of the functions of the ABC gene family and provided a basis for the role of ABC genes in grape anthocyanin transport.

Analysis of Differentially Expressed Rice Genes Reveals the ATP-Binding Cassette Transporters as Candidate Genes Against the Sheath Blight Pathogen, Rhizoctonia solani

Sheath blight is a serious rice disease worldwide, and genes involved in resistance remain unclear. In the present study, a virulent field isolate of Rhizoctonia solani was used to inoculate detached leaves of a sheath blight-resistant rice cultivar, Jasmine 85; a suppression subtractive cDNA library was constructed using RNA isolated 16 h postinoculation (hpi); and differentially expressed genes were identified from the cDNA library. A total of 159 uniquely expressed sequence tags were identified, including 105 from rice with enrichment in categories related to cellular response, molecular signaling, and host defense. Coupled with gene expression studies by DNA microarray, 27 highly induced genes involved in signal transduction and defense responses were identified within 16 hpi. Three members of the ATP-binding cassette (ABC) transporter gene family ( OsABC1, OsABC9, and OsABC12) encoding pleiotropic drug resistance-like ABC transporters were mapped to different sheath blight resistance quantitative trait loci (QTLs), and their differential expressions were validated. Three high-resolution melting (HRM) markers were developed from these ABC gene family members to distinguish alleles between sheath blight-susceptible cultivar Lemont and resistant cultivar Jasmine 85. Association of sheath blight resistance to these HRM markers was examined in 77 recombinant inbred lines derived from the cross between Jasmine 85 and Lemont. The OsABC9 gene located in a major sheath blight resistance QTL qShB9-2 showed a major contribution to sheath blight resistance. These results are useful for marker-assisted selection and functional validation of the ABC genes in sheath blight disease resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Genome-wide characterization and expression analysis of ATP-binding cassette (ABC) transporters in strawberry reveal the role of FvABCC11 in cadmium tolerance

The ATP-binding cassette (ABC) transporter is the largest gene family and is associated with the transport of various molecules, such as heavy metal ions, secondary metabolites, and phytohormones. Strawberry is an important berry fruit and a model plant for studying fleshy fruits. However, the ABC gene family has not been identified in strawberry. In present study, 115 putative ABC genes were identified in the genome of woodland strawberry (Fragaria vesca). Based on the phylogenetic analysis results, the ABC genes were grouped into eight subfamilies (6 ABCAs, 29 ABCBs, 16 ABCCs, 1 ABCDs, 2 ABCEs, 5 ABCFs, 46 ABCGs, and 10 ABCIs). Additionally, gene structure analysis revealed that the intron-exon patterns of the ABC genes are not conserved in F. vesca. Some additional conserved motifs with group specificity were found. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated ABCC subfamily gene expression across different fruit and seed developmental stages and organ profiling revealed functional diversification. Most ABCC genes exhibited preferential expression in the stems and leaves. All ABCC genes showed significant increases during the seed development stages but only ABCC8 and ABCC11 showed significant increases during fruit development. The significant changes of the 16 ABCC genes exhibited during abiotic stress treatments suggested that they might be stress-responsive genes. Over-expression of FvABCC11 in Arabidopsis partially restored seedling development under cadmium (Cd) treatment, indicated that FvABCC11 increased Cd tolerance. The results of this study provide useful information for heavy metal resistance that can be utilized to improve agricultural production.

Genome-wide identification and gene expression pattern of ABC transporter gene family in Capsicum spp.

ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three Capsicum species, i.e., Capsicum annuum, Capsicum baccatum and Capsicum chinense. Capsicum is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in C. annuum, C. baccatum and C. chinense genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location, Cis elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the Capsicum ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common cis-elements involved in the transcriptional regulation were also identified in the promoter regions of all Capsicum ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different Capsicum species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.

In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling.

ATP-binding cassette (ABC) transporters constitute one of the largest gene families in all living organisms, most of which mediate transport across biological membranes by hydrolyzing ATP. However, detailed studies of ABC transporter genes in the important oil crop, soybean, are still lacking. In the present study, we carried out genome-wide identification and phylogenetic and transcriptional analyses of the ABC gene family in G. max. A total of 261 G. max ABC (GmABCs) genes were identified and unevenly localized onto 20 chromosomes. Referring to protein-domain orientation and phylogeny, the GmABC family could be classified into eight (ABCA-ABCG and ABCI) subfamilies and ABCG were the most abundantly present. Further, investigation of whole genome duplication (WGD) signifies the role of segmental duplication in the expansion of the ABC transporter gene family in soybean. The Ka/Ks ratio indicates that several duplicated genes are governed by intense purifying selection during evolution. In addition, in silico expression analysis based on RNA-sequence using publicly available database revealed that ABC transporters are differentially expressed in tissues and developmental stages and in dehydration. Overall, we provide an extensive overview of the GmABC transporter gene family and it promises the primary basis for the study in development and response to dehydration tolerance.

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development.

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs, 20 ABCBs, 16 ABCCs, 2 ABCDs, one ABCEs, 5 ABCFs, 42 ABCGs and 9 ABCIs). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4, AcABCC7, AcABCC9, AcABCG26, AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production.

Genome-Wide Identification, Evolution, and Expression Analysis of the ATP-Binding Cassette Transporter Gene Family in Brassica rapa

ATP-binding cassette (ABC) proteins can act as transporters of different substrates across biological membranes by hydrolyzing ATP. However, little information is available about ABC transporters in Brassica rapa, an important leafy vegetable. In the present study, we carried out genome-wide identification, characterization and molecular evolution analyses of ABC gene family in B. rapa and 9 other plant species. A total of 179 B. rapa ABC genes (BraABCs) were identified. Among them, 173 BraABCs were identified on 10 chromosomes. Based on phylogenetic analysis and domain organization, the BraABC family could be grouped into eight subfamilies. BraABCs in the same subfamily showed similar motif composition and exon-intron organization. Common and unique cis-elements involved in the transcriptional regulation were also identified in the promoter regions of BraABCs. Tissue-expression analysis of BraABCs demonstrated their diverse spatiotemporal expression profiles. Influences of the whole genome triplication (WGT) on the evolution of BraABCs were studied in detail. BraABCs were preferentially retained compared with their neighboring genes during diploidization after WGT. Synteny analysis identified 76 pairs of syntenic BraABC paralogs among the three subgenomes of B. rapa, and 10 paralog pairs underwent positive selection with ω (= Ka/Ks) ratios greater than 1. Analyses of the expression patterns of syntenic BraABC paralogs pairs across five tissues and under stress treatments revealed their functional conservation, sub-functionalization, neo-functionalization and pseudogenization during evolution. Our study presents a comprehensive overview of the ABC gene family in B. rapa and will be helpful for the further functional study of BraABCs in plant growth, development, and stress responses.

Marine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature.

The ABC gene family is recognized as one of the largest gene families in all kingdoms of life. Although many genes involved in the ABC superfamily have been annotated from several fish species, information on large sets of the ABC superfamily and their evolutionary characterization are still unclear. In the marine medaka Oryzias melastigma, 50 ABC transporters were identified with bioinformatics-aided in silico analyses, and their full-length cDNA sequences were characterized. Phylogenetic analysis revealed that they could be classified into the eight subfamilies (A–H) that include all members of all ABC subfamilies. Interestingly, several teleosts’ Abcg members were closely clustered with Abch members in a distinctive clade. The abch gene was also observed in the coelacanth and the spotted gar, suggesting that this gene was retained from a bilaterian ancestor and that a gene loss event recently occurred in the tetrapod lineage. In teleosts, the nomenclature of previously annotated abcg genes should be considered carefully, as they form a distinctive clade with the marine medaka abch subfamily and other teleost abch genes, but not with the members of the Abcg subfamily.

A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis).

Salmon lice, Lepeophtheirus salmonis (Krøyer, 1837), are fish ectoparasites causing significant economic damage in the mariculture of Atlantic salmon, Salmo salar Linnaeus, 1758. The control of L. salmonis at fish farms relies to a large extent on treatment with anti-parasitic drugs. A problem related to chemical control is the potential for development of resistance, which in L. salmonis is documented for a number of drug classes including organophosphates, pyrethroids and avermectins. The ATP-binding cassette (ABC) gene superfamily is found in all biota and includes a range of drug efflux transporters that can confer drug resistance to cancers and pathogens. Furthermore, some ABC transporters are recognised to be involved in conferral of insecticide resistance. While a number of studies have investigated ABC transporters in L. salmonis, no systematic analysis of the ABC gene family exists for this species. This study presents a genome-wide survey of ABC genes in L. salmonis for which, ABC superfamily members were identified through homology searching of the L. salmonis genome. In addition, ABC proteins were identified in a reference transcriptome of the parasite generated by high-throughput RNA sequencing (RNA-seq) of a multi-stage RNA library. Searches of both genome and transcriptome allowed the identification of a total of 33 genes / transcripts coding for ABC proteins, of which 3 were represented only in the genome and 4 only in the transcriptome. Eighteen sequences were assigned to ABC subfamilies known to contain drug transporters, i.e. subfamilies B (4 sequences), C (11) and G (2). The results suggest that the ABC gene family of L. salmonis possesses fewer members than recorded for other arthropods. The present survey of the L. salmonis ABC gene superfamily will provide the basis for further research into potential roles of ABC transporters in the toxicity of salmon delousing agents and as potential mechanisms of drug resistance.

Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey.

BackgroundLampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates.ResultsWe conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed.ConclusionsThirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC gene subfamilies in chordates have undergone obvious expansion or contraction. The ABCA subfamily showed the highest gene expansion rate during chordate evolution. The evolution of ABC transporters in lampreys requires further evaluation because the present results are based on a draft genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1677-z) contains supplementary material, which is available to authorized users.

Abstract C70: ABCD3 expression in prostate and breast tumors

Abstract Background: In a previous study, we identified the ABCD3 gene as important in aggressive prostate tumors. The ABCD3 gene is a member of the ABC (ATP-Binding Cassette) family. The ABC gene family give instructions for making transporter proteins that carry many types of molecules, such as fats, sugars, protein building blocks (amino acids) and drugs, across cell membranes and is known to play a role in chemoresistance is some cancers. Purpose: Little is known about role of ABCD3 in prostate cancer, hence in the present study we assessed the expression of ABCD3 in normal and malignant prostate tissue (without regard to racial ethnicity) and determined correlations between ABCD3 expression and clinicopathologic characteristics. Methods: Clinically annotated duplicate core tissue high-density prostate adenocarcinoma tissue microarray of 92 cases of adenocarcinoma, 2 prostate transitional cell carcinoma, 12 prostate adjacent normal tissue and 8 normal prostate tissue were stained with a monoclonal antibody against ABCD3 and scored for percentage of visible staining. Results: Increased ABCD3 expression correlated with increasing Gleason score (p=0.0094), age (p=0.0014) and pathology grade (p=0.0007). Interestingly, we also observed that ABCD3 expression was elevated to varying degrees in other types of cancers, breast (stage II a), brain, cervical, head and neck, kidney and pancreatic. Conclusions: We postulate that ABCD3 may be a putative prognostic biomarker that discriminates between indolent and aggressive cancers, albeit ABCD3 function in cancer progression is still under investigation. Citation Format: R. Renee Reams, Jacqueline D. Jones, Daniel Osborne, Honghe Wang, Clayton C. Yates, III. ABCD3 expression in prostate and breast tumors. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C70. doi:10.1158/1538-7755.DISP13-C70

ABCB5 expression and cancer stem cell hypothesis in oral squamous cell carcinoma

IntroductionThe vast majority of oral cancers are squamous cell carcinomas (OSCC). The effectiveness of adjuvant cytostatic chemotherapy for OSCC is frequently restricted due to an inducible cellular mechanism called multidrug resistance (MDR) and a putative cancer stem cell (CSC) compartment in human carcinogenesis expressing multidrug efflux pumps. The novel human ATP-binding cassette (ABC) transporter ABCB5 [subfamily B (MDR/TAP) member 5] acts as an energy-dependent drug efflux transporter and marks tumour cells of a putative CSC compartment. However, to date, there is no link between ABCB5 expression and OSCC. Materials and methodsExpression of ABCB5 was analysed in OSCC specimen (n=191) and cancer cell lines (BICR3, BICR56) by immunohistochemistry, real-time polymerase chain reaction (RT-PCR) analysis and western blotting. Scanned images were digitally analysed using ImageJ and the immunomembrane plug-in. ABCB5 expression on protein level was correlated with clinical characteristics and impact on survival. ABCB5 was co-labelled with CD44 in immunohistochemical and immunofluorescence double labelling experiments. Expression subgroups were identified by receiver operating characteristics (ROC) analysis. ResultsHigh ABCB5 expression was significantly associated with tumour progression and recurrence of the tumour. Multivariate analysis demonstrated high ABCB5 expression as an independent prognostic factor (p=0.0004). Immunohistochemical and immunofluorescence double labelling experiments revealed ABCB5 expression by CD44+ cancer cells. ABCB5 specificity was confirmed by western blot and RT-PCR analysis. ConclusionsFor the first time, this study provides evidence that ABCB5 expression in OSCC might be associated with tumour formation, metastasis and a putative CSC compartment. One of the principal mechanisms for protecting putative cancer stem cells is through the expression of multifunctional efflux transporters from the ABC gene family, like ABCB5. This provides one mechanism in which putative cancer stem cells could survive and may lead to tumour relapse. Knowledge of expression profiles of ABC transporters and other genes involved in MDR will likely help therapeutic optimisation for cancer patients in clinic. However, this hypothesis requires further in vitro and in vivo studies.

Evaluation of Single Nucleotide Polymorphism Responsible for the Determination of Earwax Type in Koreans

The ABCCII gene is a member of the ATP-binding cassette gene family. A single nucleotide polymorphism (SNP) in the ABCCII gene is associated with the determination of human earwax type. The purpose of this research is to evaluate the allelic frequencies of this gene in Korean population samples. A total of 619 individuals were analyzed by Dde I restriction fragment length polymorphisms (RFLPs). The genotype frequency of dry earwax in Koreans was very high. The proportions of dry/dry genotype found were 99%(99/100) in normal controls; 98.1% (207/211) in patients with schizophrenia; 99%(99/100) in patients with breast cancer; 96%(48/50) patients with uterine myoma; 98.3%(59/60) in obesity subjects; 100%(43/43) in patients with stomach cancer, and 98.2%(54/55) in attention deficit hyperactivity disorder (ADHD) patients. The wet/wet genotype was not found. There were no significant differences in the distribution of earwax genotypes between controls and experimental groups. These results suggest that the frequency of dry earwax are very high, and therefore the SNP determining earwax type will not be useful in genetic studies of the process involved in various diseases or pathologic conditions in Korean populations.