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

Ofori, Peter Amoako; Mizuno, Ayaka; Suzuki, Mami; Martinoia, Enrico; Reuscher, Stefan; Aoki, Koh; Shibata, Daisuke; Otagaki, Shungo; Matsumoto, Shogo; Shiratake, Katsuhiro

doi:10.1371/journal.pone.0200854

Cited by 76 publications

(75 citation statements)

References 102 publications

(167 reference statements)

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“…The main difference between cereals and legumes for which PA-MRPs have been characterized so far is the gene number: While only one gene is present in diploid maize, pearl millet, and rice genomes, and three copies in the hexaploid Triticum aestivum, two and three paralogues are present in common bean and soybean, respectively [17,32,33]. The presence of more than one member of the PA-MRP genes seems to be a common feature of legumes, for example also in Medicago truncatula it is possible to predict two PA-MRP genes [35], unlike the situation in other dicotyledons, such as Arabidopsis and Solanum lycopersicum L. (tomato) in which only one PA-MRP gene was described [16,36]. As discussed below, the gene copy number has a significant influence on the lpa mutant phenotypes.…”

Section: Pa-mrp Transportersmentioning

confidence: 99%

Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants?

Cominelli

Pilu

Sparvoli

2020

Plants

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Phytic acid has two main roles in plant tissues: Storage of phosphorus and regulation of different cellular processes. From a nutritional point of view, it is considered an antinutritional compound because, being a cation chelator, its presence reduces mineral bioavailability from the diet. In recent decades, the development of low phytic acid (lpa) mutants has been an important goal for nutritional seed quality improvement, mainly in cereals and legumes. Different lpa mutations affect phytic acid biosynthetic genes. However, other lpa mutations isolated so far, affect genes coding for three classes of transporters: A specific group of ABCC type vacuolar transporters, putative sulfate transporters, and phosphate transporters. In the present review, we summarize advances in the characterization of these transporters in cereals and legumes. Particularly, we describe genes, proteins, and mutants for these different transporters, and we report data of in silico analysis aimed at identifying the putative orthologs in some other cereal and legume species. Finally, we comment on the advantage of using such types of mutants for crop biofortification and on their possible utility to unravel links between phosphorus and sulfur metabolism (phosphate and sulfate homeostasis crosstalk).

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Section: Pa-mrp Transportersmentioning

confidence: 99%

Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants?

Cominelli

Pilu

Sparvoli

2020

Plants

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“…The main members in each subfamily and the members with characteristic fruit expression patterns were revealed for further studies to elucidate the roles of CaCA family genes. Similar bioinformatics reports on other tomato transporters have had a significant impact on the many citations [58,59], and by integrating these types of studies and functional genomics, we may reveal the whole picture of fruit metabolism in the future.…”

Section: Discussionmentioning

confidence: 54%

Characterization and Expression Analysis of the Ca2+/Cation Antiporter Gene Family in Tomatoes

Amagaya

Shibuya

Nishiyama

et al. 2019

Plants

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The Ca2+/cation antiporter (CaCA) superfamily plays an important role in the regulation of the essential element Ca2+ and cation concentrations. Characterization and expression analyses of CaCA superfamily genes were performed in the tomato (Solanum lycopersicum) as a representative of dicotyledonous plants and fruit crops. Sixteen CaCA candidate genes were found and identified as tomato CaCA, SlCaCA, by a domain search. In a phylogenetic analysis of the SlCaCA superfamily, the 16 genes were classified into SlCAX, SlNCL, SlCCX, and SlMHX families. Among them, Solyc12g011070, belonging to the SlCAX family, had four splice variants, three of which were predicted to be nonfunctional because of a lack of important motifs. EF-hand domains were only found in SlNCL, in addition to consensus Na_Ca_ex domains, and the region containing EF-hand domains was characteristically long in some members of SlNCL. Furthermore, four genes of the SlCCX family were found to be intronless. As for intracellular localization, one SlCCX member was predicted to be localized to the plasma membrane, while other SlCCXs, SlCAXs, and SlMHXs were predicted to be localized to the vacuolar membrane. The expression patterns of SlCaCAs in various organs, including during several developmental stages of fruit, were classified into four groups. Genes involved in each of the SlCAX, SlNCL, and SlCCX gene families were categorized into three or four groups according to expression patterns, suggesting role sharing within each family. The main member in each subfamily and the members with characteristic fruit expression patterns included genes whose expression was regulated by sugar or auxin and that were highly expressed in a line having metabolite-rich fruit.

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“…This finding of a fewer number in the FAW genome is opposite to P450s, GSTs, CCEs, and UGTs. The ABC transporter superfamily is universally found in all organisms, including fungi, plants and animals (Ofori et al ). The ABC transporter superfamily is considered to play a major role in the ability of insects to cope with xenobiotics (Labbé et al ).…”

Section: Resultsmentioning

confidence: 99%

Genomic features of the fall armyworm (Spodoptera frugiperda) (J.E. Smith) yield insights into its defense system and flight capability

Zhou

Price

et al. 2020

Entomological Research

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The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is an agriculturally important insect pest and causes significant economic loss due to its resistance to insecticide and high dispersal ability (i.e. long‐distance flyer). We performed comparative genomics analysis based on the recently released chromosome‐scale genome of the FAW to investigate the genetic mechanisms of FAWs defense system and flight ability. The gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione‐S‐transferase, were expanded in FAW, enabling its ability to detect and detoxify many plant secondary compounds. The chromosomal locations of five detoxification‐related genes (i.e. ABC, CCE, GST, P450, and UGT) were analyzed, which revealed the density of these genes across the FAW genome. Several genes like Mio, Sik2, CRTC, and Lpin were positively selected in FAW, which were associated with energy metabolism, lipid metabolism, and/or muscle development, and thus possibly contributed to the high flight ability of FAW. We also analyzed the homologs to antimicrobial genes reported in the Drosophila genome, and identified 2 attacins, 6 cecropins, 3 gloverins, and 2 moricins in FAW. The findings of this study will broadly expand our knowledge on the biology of the devastating FAW, and contribute to the development of new pest management strategies for the control of major agricultural pests like FAW.

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

Cited by 76 publications

References 102 publications

Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants?

Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants?

Characterization and Expression Analysis of the Ca2+/Cation Antiporter Gene Family in Tomatoes

Genomic features of the fall armyworm (Spodoptera frugiperda) (J.E. Smith) yield insights into its defense system and flight capability

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