OsNPF3.1, a nitrate,
abscisic acid and gibberellin transporter gene, is essential for rice tillering
and nitrogen utilization efficiency

doi:10.1016/j.jia.2023.04.024

Journal of Integrative Agriculture

2024, Vol. 23

Issue (04): 1087-1104 DOI: 10.1016/j.jia.2023.04.024

Crop Science

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OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency

Junnan Hang^1*, Bowen Wu^1*, Diyang Qiu^{2, 3*}, Guo Yang¹, Zhongming Fang^1#, Mingyong Zhang^2#

¹Institute of Rice Industry Technology Research/Key Laboratory of Functional Agriculture, Guizhou Provincial Department of Education/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education/Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/College of Agricultural Sciences, Guizhou University, Guiyang 550025, China

²Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement/Guangdong Provincial Key Laboratory of Applied Botany/South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China

³Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China

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摘要

低亲和硝酸盐转运基因成员已在水稻硝酸盐转运基因1/肽转运基因家族（NPF）的4-8亚家族中鉴定出来，但OsNPF3亚家族在硝酸盐和植物激素转运及水稻生长发育上还不清楚。本研究中，我们发现硝酸盐和植物激素转运基因OsNPF3.1在水稻分蘖和氮利用效率上起重要作用。OsNPF3.1的启动子序列在517个水稻品种中具有4种主要单倍型，其表达与分蘖数呈正相关。OsNPF3.1在水稻基部、茎和叶片中的表达量高于其他部位，且在水稻根部和地上部分被硝酸盐、脱落酸（ABA）和赤霉素3（GA3）强烈诱导表达。电生理实验表明，OsNPF3.1是一种pH依赖的低亲和硝酸盐转运基因，且水稻原生质体摄取实验表明它是ABA和GA3的转运基因。OsNPF3.1过表达后在高硝态氮浓度下显著促进了ABA在根系的积累和GA在基部的积累，进一步抑制了腋芽的伸长和水稻分蘖。在中低硝态氮浓度下OsNPF3.1的过表达植株氮利用效率增强，而在高硝态氮浓度下OsNPF3.1的突变体植株氮利用效率增加。以上结果表明，OsNPF3.1在不同硝态氮浓度下的不同水稻组织中转运硝酸盐和植物激素。OsNPF3.1表达改变的过表达植株或CRISPR植株分别在低硝酸盐和高硝酸盐浓度下提高氮利用效率。

Abstract

Low-affinity nitrate transporter genes have been identified in subfamilies 4–8 of the rice nitrate transporter 1 (NRT1)/peptide transporter family (NPF), but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown. In this study, we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency (NUtE). OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars, and its expression is positively associated with tiller number. Its expression was higher in the basal part, culm, and leaf blade than in other parts of the plant, and was strongly induced by nitrate, abscisic acid (ABA) and gibberellin 3 (GA₃) in the root and shoot of rice. Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter, with rice protoplast uptake assays showing it to be an ABA and GA₃ transporter. OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering, especially at high nitrate concentrations. The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations, whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats (CRISPR) plants was increased under high nitrate concentrations. The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations. The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations, respectively.

Keywords: rice tillering grain yield phytohormone nitrate transporter nitrogen utilization efficiency

Online: 13 February 2023 Accepted: 20 March 2023

Fund:

We thank Chen Y and Miller A at John Innes Centre, UK, for assistance with the functional analysis of OsNPF3.1 in Xenopus laevis oocytes. This research was supported by the the Guizhou Provincial Excellent Young Talents Project of Science and Technology, China (YQK (2023) 002), the Guizhou Provincial Science and Technology Projects, China ((2022) Key 008), the Guizhou Provincial Science and Technology Support Plan, China ((2022) Key 026), the Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, China ((2023) 008), and the Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions, China ((2023) 007).

About author: #Correspondence Zhongming Fang, E-mail: zmfang@gzu.edu.cn; Mingyong Zhang, E-mail: zhangmy@scbg.ac.cn * These authors contributed equally to this study

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Junnan Hang, Bowen Wu, Diyang Qiu, Guo Yang, Zhongming Fang, Mingyong Zhang. 2024.

OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency . Journal of Integrative Agriculture, 23(04): 1087-1104.

Agharkar M, Lomba P, Altpeter F, Zhang H N, Kenworthy K, Lange T. 2007. Stable expression of AtGA2ox1 in a low-input turfgrass (Paspalum notatum Flugge) reduces bioactive gibberellin levels and improves turf quality under field conditions. Plant Biotechnology Journal, 5, 791–801.

Binenbaum J, Weinstain R, Shani E. 2018. Gibberellin localization and transport in plants. Trends in Plant Science, 23, 410–421.

Boursiac Y, Léran S, Corratgé-Faillie C, Gojon A, Krouk G, Lacombe B. 2013. ABA transport and transporters. Trends in Plant Science, 18, 325–333.

Cai H M, Zhou Y, Xiao J H, Li X H, Zhang Q F, Lian X M. 2009. Overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice. Plant Cell Reports, 28, 527–537.

Chen W, Gao Y Q, Xie W B, Gong L, Lu K, Wang W S, Li Y, Liu X Q, Zhang H Y, Dong H X, Zhang W, Zhang L J, Yu S B, Wang G W, Lian X M, Luo J. 2014. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics, 46, 714.

David L C, Berquin P, Kanno Y, Seo M, Daniel-Vedele F, Ferrario-Méry S. 2016. N availability modulates the role of NPF3.1, a gibberellin transporter, in GA-mediated phenotypes in Arabidopsis. Planta, 244, 1315–1328.

Fan X R, Xie D, Chen J G, Lu H Y, Xu Y L, Ma C, Xu G H. 2014. Over-expression of OsPTR6 in rice increased plant growth at different nitrogen supplies but decreased nitrogen use efficiency at high ammonium supply. Plant Science, 227, 1–11.

Fang Z M, Bai G X, Huang W T, Wang Z X, Wang X L, Zhang M Y. 2017. The rice peptide transporter OsNPF7.3 is induced by organic nitrogen, and contributes to nitrogen allocation and grain yield. Frontiers in Plant Science, 8, 1338.

Fang Z M, Xia K F, Yang X, Grotemeyer M S, Meier S, Rentsch D, Xu X L, Zhang M Y. 2013. Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnology Journal, 11, 446–458.

Glass A D M, Shaff J E, Kochian L V. 1992. Studies of the uptake of nitrate in barley: IV. Electrophysiology. Plant Physiology, 99, 456–463.

Guan Y, Liu D F, Qiu J, Liu Z J, He Y N, Fang Z J, Huang X H, Gong J M. 2022. The nitrate transporter OsNPF7.9 mediates nitrate allocation and the divergent nitrate use efficiency between indica and japonica rice. Plant Physiology, 189, 215–229.

Hu B, Wang W, Ou S J, Tang J Y, Li H, Che R H, Zhang Z H, Chai X Y, Wang H R, Wang Y Q, Liang C Z, Liu L C, Piao Z Z, Deng Q Y, Deng K, Xu C, Liang Y, Zhang L H, Li L G, Chu C C. 2015. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nature Genetics, 47, 834–838.

Hu R, Qiu D Y, Chen Y, Miller A J, Fan X R, Pan X P, Zhang M Y. 2016. Knock-down of a tonoplast localized low-affinity nitrate transporter OsNPF7.2 affects rice growth under high nitrate supply. Frontiers in Plant Science, 7, 1529.

Huang L J, Luo J J, Wang Y K, Li N. 2021. From green revolution to green balance: the nitrogen and gibberellin mediated rice tiller growth. Plant Signaling & Behavior, 16, 1917838.

Huang W T, Bai G X, Wang J, Zhu W, Zeng Q S, Lu K, Sun S Y, Fang Z M. 2018. Two splicing variants of OsNPF7.7 regulate shoot branching and nitrogen utilization efficiency in rice. Frontiers in Plant Science, 9, 300.

Huang W T, Nie H P, Feng F, Wang J, Lu K, Fang Z M. 2019. Altered expression of OsNPF7.1 and OsNPF7.4 differentially regulates tillering and grain yield in rice. Plant Science, 283, 23–31.

Ishimaru Y, Washiyama K, Oikawa T, Hamamoto S, Uozumi N, Ueda M. 2017. Dimerization of GTR1 regulates their plasma membrane localization. Plant Signaling & Behavior, 12, e1334749.

Kanno Y, Hanada A, Chiba Y, Ichikawa T, Nakazawa M, Matsui M, Koshiba T, Kamiya Y, Seo M. 2012. Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor. Proceedings of the National Academy of Sciences of the United States of America, 109, 9653–9658.

Kanno Y, Kamiya Y, Seo M. 2013. Nitrate does not compete with abscisic acid as a substrate of AtNPF4.6/NRT1.2/AIT1 in Arabidopsis. Plant Signaling & Behavior, 8, e26624.

Kanno Y, Oikawa T, Chiba Y, Ishimaru Y, Shimizu T, Sano N, Koshiba T, Kamiya Y, Ueda M, Seo M. 2016. AtSWEET13 and AtSWEET14 regulate gibberellin-mediated physiological processes. Nature Communications, 7, 13245.

Kramer E M. 2006. How far can a molecule of weak acid travel in the apoplast or xylem? Plant Physiology, 141, 1233–1236.

Léran S, Noguero M, Corratgé-Faillie C, Boursiac Y, Brachet C, Lacombe B. 2020. Functional characterization of the Arabidopsis abscisic acid transporters NPF4.5 and NPF4.6 in Xenopus oocytes. Frontiers in Plant Science, 11, 144.

Li H, Hu B, Chu C C. 2017. Nitrogen use efficiency in crops: Lessons from Arabidopsis and rice. Journal of Experimental Botany, 68, 2477–2488.

Li S B, Qian Q, Fu Z M, Zeng D L, Meng X B, Kyozuka J, Maekawa M, Zhu X D, Zhang J, Li J Y, Wang Y H. 2009. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. The Plant Journal, 58, 592–605.

Li Y G, Ouyang J, Wang Y Y, Hu R, Xia K F, Duan J, Wang Y Q, Tsay Y F, Zhang M Y. 2015. Disruption of the rice nitrate transporter OsNPF2.2 hinders root-to-shoot nitrate transport and vascular development. Scientific Reports, 5, 9635.

Lin C M, Koh S, Stacey G, Yu S M, Lin T Y, Tsay Y F. 2000. Cloning and functional characterization of a constitutively expressed nitrate transporter gene, OsNRT1, from rice. Plant Physiology, 122, 379–388.

Lin S H, Kuo H F, Canivenc G, Lin C S, Lepetit M, Hsu P K, Tillard P, Lin H L, Wang Y Y, Tsai C B, Gojon A, Tsay Y F. 2008. Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport. The Plant Cell, 20, 2514–2528.

Luo L, Takahashi M, Kameoka H, Qin R Y, Shiga T, Kanno Y, Seo M, Itoh M, Xu G H, Kyozuka J. 2019. Developmental analysis of the early steps in strigolactone-mediated axillary bud dormancy in rice. The Plant Journal, 97, 1006–1021.

Ma X L, Liang Z X. 1997. Studies on the effects of endogeneous hormones in winter wheat tillers during the course of senesence. Acta Agronomica Sinica, 23, 200–207. (in Chinese)

Mauriat M, Sandberg L G, Moritz T. 2011. Proper gibberellin localization in vascular tissue is required to control auxin-dependent leaf development and bud outgrowth in hybrid aspen. The Plant Journal, 67, 805–816.

Pan W Q, Liang J H, Sui J J, Li J R, Liu C, Xin Y, Zhang Y M, Wang S K, Zhao Y J, Zhang J, Yi M F, Gazzarrini S, Wu J. 2021. ABA and bud dormancy in perennials: Current knowledge and future perspective. Genes, 12, 1635.

Pike S, Gao F, Kim M J, Kim S H, Schachtman D P, Gassmann W. 2014. Members of the NPF3 transporter subfamily encode pathogen-inducible nitrate/nitrite transporters in grapevine and Arabidopsis. Plant Cell and Physiology, 55, 162–170.

Saito H, Oikawa T, Hamamoto S, Ishimaru Y, Kanamori-Sato M, Sasaki-Sekimoto Y, Utsumi T, Chen J, Kanno Y, Masuda S, Kamiya Y, Seo M, Uozumi N, Ueda M, Ohta H. 2015. The jasmonate-responsive GTR1 transporter is required for gibberellin-mediated stamen development in Arabidopsis. Nature Communications, 6, 6095.

Shabala S, White R G, Djordjevic M A, Ruan Y L, Mathesius U. 2015. Root-to-shoot signalling: Integration of diverse molecules, pathways and functions. Functional Plant Biology, 43, 87–104.

Shimizu T, Kanno Y, Suzuki H, Watanabe S, Seo M. 2021. Arabidopsis NPF4.6 and NPF5.1 control leaf stomatal aperture by regulating abscisic acid transport. Genes, 12, 885.

Sousa R T, Paiva A L S, Carvalho F E L, Alencar V T C B, Silveira J A G. 2021. Ammonium overaccumulation in senescent leaves as a novel exclusion mechanism to avoid toxicity in photosynthetically active rice leaves. Environmental and Experimental Botany, 186, 104452.

Su J, Xu K, Wu C, Li Z R, Hu Z L, Zheng X F, Song S F, Tang W B, Tang Z H, Li L Z. 2021. Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential. Scientific Reports, 11, 6894.

Sun H Y, Qian Q, Wu K, Luo J J, Wang S S, Zhang C W, Ma Y F, Liu Q, Huang X D, Yuan Q B, Han R X, Zhao M, Dong G J, Guo L B, Zhu X D, Gou Z H, Wang W, Wu Y J, Lin H X, Fu X D. 2014. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice. Nature Genetics, 46, 652–656.

Tal I, Zhang Y, Jørgensen M E, Pisanty O, Barbosa I C R, Zourelidou M, Regnault T, Crocoll C, Olsen C E, Weinstain R, Schwechheimer C, Halkier B A, Nour-Eldin H H, Estelle M, Shani E. 2016. The Arabidopsis NPF3 protein is a GA transporter. Nature Communications, 7, 11486.

Tang W J, Ye J, Yao X M, Zhao P Z, Xuan W, Tian Y L, Zhang Y Y, Xu S, An H Z, Chen G M, Yu J, Wu W, Ge Y W, Liu X L, Li J, Zhang H Z, Zhao Y Q, Yang B, Jiang X Z, Peng C, et al. 2019. Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice. Nature Communications, 10, 5279.

Tegeder M. 2014. Transporters involved in source to sink partitioning of amino acids and ureides: Opportunities for crop improvement. Journal of Experimental Botany, 65, 1865–1878.

Tsay Y F, Chiu C C, Tsai C B, Ho C H, Hsu P K. 2007. Nitrate transporters and peptide transporters. FEBS Letters, 581, 2290–2300.

Wang B, Smith S M, Li J Y. 2018. Genetic regulation of shoot architecture. Annual Review of Plant Biology, 69, 437–468.

Wang J, Lu K, Nie H P, Zeng Q S, Wu B W, Qian J J, Fang Z M. 2018. Rice nitrate transporter OsNPF7.2 positively regulates tiller number and grain yield. Rice, 11, 12.

Wang J, Wan R J, Nie H P, Xue S W, Fang Z M. 2022. OsNPF5.16, a nitrate transporter gene with natural variation, is essential for rice growth and yield. The Crop Journal, 10, 397–406.

Wang R N, Qian J J, Fang Z M, Tang J H. 2020. Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth. BMC Plant Biology, 20, 197.

Wang S S, Chen A Q, Xie K, Yang X F, Luo Z Z, Chen J D, Zeng D C, Ren Y H, Yang C F, Wang L X, Feng H M, López-Arredondo D L, Herrera-Estrella L R, Xu G H. 2020. Functional analysis of the OsNPF4.5 nitrate transporter reveals a conserved mycorrhizal pathway of nitrogen acquisition in plants. Proceedings of the National Academy of Sciences of the United States of America, 117, 16649–16659.

Wang Y H, Li J Y. 2008. Molecular basis of plant architecture. Annual Review of Plant Biology, 59, 253–279.

Wei C L, Cao B S, Hua S, Li B G. 2022. Quantitative analysis of the effect of the PAY1 gene on rice canopy structure during different reproductive stages. Journal of Integrative Agriculture, 21, 3488–3500.

Xia X D, Fan X R, Wei J, Feng H M, Qu H Y, Xie D, Miller A J, Xu G H. 2015. Rice nitrate transporter OsNPF2.4 functions in low-affinity acquisition and long-distance transport. Journal of Experimental Botany, 66, 317–331.

Xin W, Zhang L N, Gao J P, Zhang W Z, Yi J, Zhen X X, Bi C Y, He D W, Liu S M, Zhao X Y. 2021. Adaptation mechanism of roots to low and high nitrogen revealed by proteomic analysis. Rice, 14, 5.

Xing Y Z, Zhang Q F. 2010. Genetic and molecular bases of rice yield. Annual Review of Plant Biology, 61, 421–442.

Xu J, Shang L G, Wang J J, Chen M M, Fu X, He H Y, Wang Z A, Zeng D L, Zhu L, Hu J, Zhang C, Chen G, Gao Z Y, Zou W W, Ren D Y, Dong G J, Shen L, Zhang Q, Li Q, Guo L B, et al. 2021. The seedling biomass 1 allele from indica rice enhances yield performance under low-nitrogen environments. Plant Biotechnology Journal, 19, 1681–1683.

Yang X H, Nong B X, Chen C, Wang J R, Xia X Z, Zhang Z Q, Wei Y, Zeng Y, Feng R, Wu Y Y, Guo H, Yan H F, Liang Y T, Liang S H, Yan Y, Li D T, Deng G F. 2023. OsNPF3.1, a member of the NRT1/PTR family, increases nitrogen use efficiency and biomass production in rice. The Crop Journal, 11, 108–118.

Zhang H, Liu K, Wang Z Q, Liu L J, Yang J C. 2015. Abscisic acid, ethylene and antioxidative systems in rice grains in relation with grain filling subjected to postanthesis soil-drying. Plant Growth Regulation, 76, 135–146.

Zhang Q Q, Wang J G, Wang L Y, Wang J F, Wang Q, Yu P, Bai M Y, Fan M. 2020. Gibberellin repression of axillary bud formation in Arabidopsis by modulation of DELLA-SPL9 complex activity. Journal of Integrative Plant Biology, 62, 421–432.

Zhong Y Q W, Hu J H, Xia Q M, Zhang S L, Li X, Pan X Y, Zhao R P, Wang R W, Yan W M, Shangguan Z P, Hu F Y, Yang C D, Wang W. 2020. Soil microbial mechanisms promoting ultrahigh rice yield. Soil Biology & Biochemistry, 143, 107741.

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