Genome-wide identification of ATP-binding cassette ( ABC ) transporters and conservation of their xenobiotic transporter function in the monogonont rotifer ( Brachionus koreanus )

2017 ◽  
Vol 21 ◽  
pp. 17-26 ◽  
Author(s):  
Chang-Bum Jeong ◽  
Hui-Su Kim ◽  
Hye-Min Kang ◽  
Young Hwan Lee ◽  
Bingsheng Zhou ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Atp Binding ◽  
Genome Wide ◽  
Brachionus Koreanus ◽  
Monogonont Rotifer ◽  
Atp Binding Cassette

scholarly journals Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0200854 ◽  
Author(s):  
Peter Amoako Ofori ◽  
Ayaka Mizuno ◽  
Mami Suzuki ◽  
Enrico Martinoia ◽  
Stefan Reuscher ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Atp Binding ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Atp Binding Cassette

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

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Awdhesh Kumar Mishra ◽  
Jinhee Choi ◽  
Muhammad Fazle Rabbee ◽  
Kwang-Hyun Baek
Keyword(s):  
Gene Family ◽  
Abc Transporter ◽  
Abc Transporters ◽  
In Silico ◽  
Gene Families ◽  
Protein Domain ◽  
Atp Binding ◽  
Transporter Gene ◽  
Genome Wide ◽  
Atp Binding Cassette

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.

scholarly journals Genome-wide analysis of ATP-binding cassette transporters sheds light on the genes related to bioactive metabolite transportation in Salvia miltiorrhiza

2020 ◽  
Author(s):  
Li Yan ◽  
Jianhong Zhang ◽  
Hongyu Chen ◽  
Luo Hongmei
Keyword(s):  
Medicinal Plant ◽  
Candidate Genes ◽  
Abc Transporters ◽  
Salvia Miltiorrhiza ◽  
Atp Binding ◽  
Bioactive Metabolite ◽  
Salvianolic Acid ◽  
Genome Wide ◽  
In Cells ◽  
Atp Binding Cassette

Abstract Background: ATP-binding cassette (ABC) transporters have been found in plants and play important roles in metabolic transport in cells, which affect the subcellular compartmentalisation and tissue distribution of these compounds in particular. The dry roots and rhizomes of Salvia miltiorrhiza Bunge, a widely used medicinal plant, known as Danshen in traditional Chinese medicine, contain biologically active secondary metabolites of tanshinone and salvianolic acid. Given an assembled and annotated genome and a set of transcriptome data of S. miltiorrhiza, we analysed and identified the candidate genes that likely involved in the bioactive metabolite transportation of this medicinal plant, starting with the members of the ABC transporter family.Results: A total of 114 genes encoding ABC transporters were identified in the genome of S. miltiorrhiza. All the ABC genes were divided into eight subfamilies, including 3ABCA, 31ABCB, 14ABCC, 2ABCD, 1ABCE, 7ABCF, 46ABCG and 10 ABCI. Gene expressional profiling analysis revealed the tissue-specific expression profiles of these ABC transporters, particularly the highly expressed transporters in the roots of S. miltiorrhiza, which might be involved in transporting bioactive compounds of this medicinal plant. Notably, 18 genes that were highly expressed in the roots of S. miltiorrhiza were selected and verified by quantitative reverse transcription polymerase chain reaction to determine the co-expression profiling of these candidate genes with the key enzyme genes involved in the tanshinone and salvianolic acid biosynthetic pathways. Finally, three ABC genes (SMil_00020022, SMil_00010949, SMil_00027268) and one gene (SMil_00016361) might be involved in tanshinone and salvianolic acid transport in cells, respectively. In addition, the biological functions of S. miltiorrhiza ABC transporters were predicted on the basis of the phylogenetic analysis and expressional profile exploration, including the transportation of lipids, hormones, ions and primary metabolites.Conclusions: Our systematic analyses on the ABC transporters in S. miltiorrhiza provided information on ABC proteins for the first time and revealed the candidate transporters involved in the bioactive compound transportation of this medicinal plant. The genome-wide identification, transcriptome profile analysis and their phylogenetic relationships would provide a new perspective on the function of ABC transporters in S. miltiorrhiza.

scholarly journals Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Li Yan ◽  
Jianhong Zhang ◽  
Hongyu Chen ◽  
Hongmei Luo
Keyword(s):  
Medicinal Plant ◽  
Abc Transporters ◽  
Phylogenetic Relationships ◽  
Salvia Miltiorrhiza ◽  
Atp Binding ◽  
Biological Functions ◽  
Bioactive Metabolite ◽  
Salvianolic Acid ◽  
Genome Wide ◽  
Atp Binding Cassette

Abstract Background ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic compounds. Salvia miltiorrhiza Bunge, known as Danshen in traditional Chinese medicine, is a highly valued medicinal plant used to treat cardiovascular and cerebrovascular diseases. The dry roots and rhizomes of S. miltiorrhiza contain biologically active secondary metabolites of tanshinone and salvianolic acid. Given an assembled and annotated genome and a set of transcriptome data of S. miltiorrhiza, we analysed and identified the candidate genes that likely involved in the bioactive metabolite transportation of this medicinal plant, starting with the members of the ABC transporter family. Results A total of 114 genes encoding ABC transporters were identified in the genome of S. miltiorrhiza. All of these ABC genes were divided into eight subfamilies: 3ABCA, 31ABCB, 14ABCC, 2ABCD, 1ABCE, 7ABCF, 46ABCG, and 10 ABCI. Gene expression analysis revealed tissue-specific expression profiles of these ABC transporters. In particular, we found 18 highly expressed transporters in the roots of S. miltiorrhiza, which might be involved in transporting the bioactive compounds of this medicinal plant. We further investigated the co-expression profiling of these 18 genes with key enzyme genes involved in tanshinone and salvianolic acid biosynthetic pathways using quantitative reverse transcription polymerase chain reaction (RT-qPCR). From this RT-qPCR validation, we found that three ABC genes (SmABCG46, SmABCG40, and SmABCG4) and another gene (SmABCC1) co-expressed with the key biosynthetic enzymes of these two compounds, respectively, and thus might be involved in tanshinone and salvianolic acid transport in root cells. In addition, we predicted the biological functions of S. miltiorrhiza ABC transporters using phylogenetic relationships and analysis of the transcriptome to find biological functions. Conclusions Here, we present the first systematic analysis of ABC transporters in S. miltiorrhiza and predict candidate transporters involved in bioactive compound transportation in this important medicinal plant. Using genome-wide identification, transcriptome profile analysis, and phylogenetic relationships, this research provides a new perspective on the critical functions of ABC transporters in S. miltiorrhiza.

Sign in / Sign up

Export Citation Format

Share Document