Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa1 in rice

Lu, Haiping; Pang, Wei-qin; Li, Wen-xu; Tan, Yuanyuan; Wang, Qing; Zhao, Haijun; Shu, Qingyao

doi:10.1631/jzus.b1500205

Cited by 4 publications

(4 citation statements)

References 35 publications

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“…However, RT-PCR analysis of OsLpa 1 locus revealed that OsLpa 1-3.1 expression exhibited both vegetative and seed specificity, which indicates a major role of OsLpa 1-3.1 in PA biosynthesis; however, OsLpa 1-3.2 and OsLpa 1-3.3 showed significant and dynamic changes at 15 DAG and 5 DAF, respectively ( Fig 5A ), suggesting that these variants may play important roles in seedling growth and seed development, respectively. This finding is consistent with a previous study in rice [ 52 ]. Additionally, we investigated the expression of OsLpa 1 paralog on chromosome 9 (Os09g0572200), that encodes a protein homology to OsLpa 1-3 and a IPK2 kinase is specific for the lipid dependent pathway, OsIpk 2 (Os02g0523800), in spikelets at 5 DAF, to provide an alternative explanation for the low level of PA in lpa mutant seeds.…”

Section: Discussionsupporting

confidence: 94%

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Kishor

Lee

et al. 2019

PLoS ONE

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In plants, myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytic acid (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral cations, resulting in mineral deficiencies among brown rice consumers. Therefore, considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acidsubstitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure indicated that myo-inositol 3-monophosphate [Ins(3)P1] could bind to the active site of Lpa1, with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA biosynthesis.

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Section: Discussionsupporting

confidence: 94%

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Kishor

Lee

et al. 2019

PLoS ONE

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“…Candidate gene sequencing (Fig 4) and co-segregation analysis (Fig 7 and Table 6) however, OsLpa1-3.2 and OsLpa1-3.3 showed significant and dynamic changes at 15 DAG and 5 DAF, respectively (Fig 5A), suggesting that these variants play important roles in seedling growth and seed development, respectively. This finding is consistent with a previous study in rice [52]. Additionally, we investigated the expression of OsLpa1 paralog (Os09g0572200) and a IPK2 kinase is specific for the lipid independent pathway, OsIpk2…”

Section: Biocomputational Analysissupporting

confidence: 91%

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Kishor

Lee

et al. 2018

Preprint

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21In plants, 2,3,4,5, ), also known as phytic acid 22 (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total 2 23 P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral 24 cations, resulting in mineral deficiencies among brown rice consumers. Therefore, 25 considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In 26 this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis 27 gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice 28 cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, 29 at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA 30 content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of 31 the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acid 32 substitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure 33 indicated that myo-inositol 3-monophosphate [Ins(3)P 1 ] kinase binds to the active site of Lpa1, 34 with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent 35 to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in 36 regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile 37 substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA 38 biosynthesis. 39 40 42 phytic acid (PA), is considered a major source of phosphorus (P) available in the form of 43 phytate, and accounts for 65-85% of the total P in seeds [1]. Monogastric animals poorly digest 44 PA, as they lack the phytase enzyme, which is responsible for the release of phosphate residues 45 [2]. PA is an efficient chelator of mineral cations, such as zinc (Zn 2+ ), iron (Fe 2+ ), magnesium 46 (Mg 2+ ), potassium (K 2+ ), and calcium (Ca 2+ ), in the nutritional tract. Because of these attributes, 3 47 PA is considered as an antinutrient [3, 4]. Hence, there is a need to develop low PA (LPA) crop 48 cultivars to maximize the nutritional benefits of grains. 49 Mutants associated with the LPA phenotype have been identified in several crop plants 50 including maize (Zea mays) [5, 6], barley (Hordeum vulgare) [7], soyabean (Glycine max) [8], 51 rice (Oryza sativa) [9], and wheat (Triticum aestivum) [10]. Although, LPA mutants are 52identified primarily on the basis of percentage reduction of PA and high inorganic P (P i ) content 53 in seeds [5, 11], some mutants show a significant accumulation of myo-inositol and inositol 54 phosphate [Ins(1,3,4)P 3 5-/6] intermediates in seeds [12, 13]. 55Previously, the LPA phenotype of seeds has been associated with reduced agronomic 56 performance of mutant crop plants in the field [5, 14]. It is important to understand the genetic 57 and molecular bases of reduced agronomic performance of LPA mutants for ef...

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“…Since the biochemical function of the 2‐PGK2 protein is largely unknown in plant species (Lu et al , ; Kishor et al , ), the novel bn2‐pgk2 mutants can be used to investigate its biochemical properties in the phytic acid pathway in B. napus . Since we have not seen pleiotropic effects on plant growth and thousand kernel weights between the mutants and the controls there are no adverse effects of the induced mutations (Table S4).…”

Section: Discussionmentioning

confidence: 99%

“…1). It was hypothesized that this enzyme, in addition to producing 2,3-bisphosphoglycerate, uses myo-inositol monophosphate as a substrate, resulting in the synthesis of inositol bisphosphate (Raboy, 2007;Lu et al, 2016). The enzyme was initially identified in rice, and knockout mutants are available from rice and Arabidopsis, which showed a phytic acid reduction of 45% and 57%, respectively (Kim et al, 2008;Kim & Tai, 2011;Kishor et al, 2019).…”

Section: Analysis Of Phytic Acid Contents In Single and Double Mutantsmentioning

confidence: 99%

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

Sashidhar

Harloff

2019

New Phytologist

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Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants.We implemented a high-throughput next-generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2-PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene.A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2-PGK2 showed a significant reduction of phytic acid contents.We propose to use three-dimensional pooling combined with amplicon stacking and nextgeneration sequencing to identify mutations in polyploid oilseed rape in a fast and cost-effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2-PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.

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Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa1 in rice

Cited by 4 publications

References 35 publications

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

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