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RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. [1]

Annotated Information


rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference [1]).

Role of hypodermal suberin under waterlogged conditions Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution. Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils [2]. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils [2] [3]. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil [4] [5] [6]. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions. In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma [3]. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis. But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma. A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution. Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions. Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers. Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier [7] [8]. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers. On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions. In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 [9][10], while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls [9]. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths, as was previously reported for rice root suberin [9][10]. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments [10], which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions. In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions. Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis [11] and maize [9], which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 [3]. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference [1]).

RCN1/OsABCG5 is involved in hypodermal suberization Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane [5][12][13]. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes [12]. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes [14][15][16][17]. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation [18]. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported [18] [11] reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 [11]. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root [17]. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis). Furthermore, hypodermal suberization declined in both of the rcn1 mutants. These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis. Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis. In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions. However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis. Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis and had noticeably abnormal root systems. The rcn1 mutants were originally isolated by their smaller number of culms [19]. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants. The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins [19], it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members [20] [21] [22]. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.


A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference [1]).

two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype [19]. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively [19]. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air). This phenotype was more severe in rcn1-2. rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions. In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions or in well-aerated nutrient solution, suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.


RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference [1]).

RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions. In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions. To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues. The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions. To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions. Moreover, GUS activity was observed in the hypodermis and the endodermis of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells, suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

Labs working on this gene

1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan 2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan 3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan 4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan 5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan 6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany 7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan 8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan 9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan 10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan 11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan


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