SpringerLink
Log in

An alanine to valine mutation of glutamyl-tRNA reductase enhances 5-aminolevulinic acid synthesis in rice

  • Original Article
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

An alanine to valine mutation of glutamyl-tRNA reductase’s 510th amino acid improves 5-aminolevulinic acid synthesis in rice.

Abstract

5-aminolevulinic acid (ALA) is the common precursor of all tetrapyrroles and plays an important role in plant growth regulation. ALA is synthesized from glutamate, catalyzed by glutamyl-tRNA synthetase (GluRS), glutamyl-tRNA reductase (GluTR), and glutamate-1-semialdehyde aminotransferase (GSAT). In Arabidopsis, ALA synthesis is the rate-limiting step in tetrapyrrole production via GluTR post-translational regulations. In rice, mutations of GluTR and GSAT homologs are known to confer chlorophyll deficiency phenotypes; however, the enzymatic activity of rice GluRS, GluTR, and GSAT and the post-translational regulation of rice GluTR have not been investigated experimentally. We have demonstrated that a suppressor mutation in rice partially reverts the xantha trait. In the present study, we first determine that the suppressor mutation results from a G → A nucleotide substitution of OsGluTR (and an A → V change of its 510th amino acid). Protein homology modeling and molecular docking show that the OsGluTRA510V mutation increases its substrate binding. We then demonstrate that the OsGluTRA510V mutation increases ALA synthesis in Escherichia coli without affecting its interaction with OsFLU. We further explore homologous genes encoding GluTR across 193 plant species and find that the amino acid (A) is 100% conserved at the position, suggesting its critical role in GluTR. Thus, we demonstrate that the gain-of-function OsGluTRA510V mutation underlies suppression of the xantha trait, experimentally proves the enzymatic activity of rice GluRS, GluTR, and GSAT in ALA synthesis, and uncovers conservation of the alanine corresponding to the 510th amino acid of OsGluTR across plant species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive BIG Data Center, Bei**g Institute of Genomics (BIG), and Chinese Academy of Sciences under BioProject number PRJCA007389, publicly accessible at https://bigd.big.ac.cn/gsa/.

References

  • Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178

    Article  CAS  PubMed  Google Scholar 

  • Akram NA, Ashraf M (2013) Regulation in plant stress tolerance by a potential plant growth regulator, 5-aminolevulinic acid. J Plant Growth Regul 32:663–679

    Article  CAS  Google Scholar 

  • Alzohairy AM (2011) Bioedit: an important software for molecular biology. GERF Bull Biosci 2:60–61

    Google Scholar 

  • Apitz J, Kenji NK, Schmied J, Wolf A, Hedtke B, Van WKJ, Grimm B (2016) Posttranslational control of ALA synthesis includes GluTR degradation by Clp protease and stabilization by GluTR-binding protein. Plant Physiol 170:1289–1298

    Article  CAS  Google Scholar 

  • Beale SI (1999) Enzymes of chlorophyll biosynthesis. Photosynth Res 60:43–73

    Article  CAS  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland GL, Bourne PE (2000) The protein data bank. Nucl Acids Res 28:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Shen J, Zhang L, Qi H, Yang L, Wang H, Wang J, Wang Y, Du H, Tao Z, Zhao T, Deng P, Shu Q, Qian Q, Yu H, Song S (2021) Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought tolerance in rice. Mol Plant 14:1297–1311

    Article  CAS  PubMed  Google Scholar 

  • Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly (austin) 6:80–92

    Article  CAS  Google Scholar 

  • Czarnecki O, Hedtke B, Melzer M, Rothbart M, Richter A, Schroter Y, Pfannschmidt T, Grimm B (2011) An Arabidopsis GluTR ation of 5-aminolevulinic acid synthbinding protein mediates spatial separesis in chloroplasts. Plant Cell 23:4476–4491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai S, Wang BQ, Song Y, **e ZM, Li C, Li S, Huang Y, Jiang M (2021) Astaxanthin and its gold nanoparticles mitigate cadmium toxicity in rice by inhibiting cadmium translocation and uptake. Sci Total Environ 786:147496

    Article  CAS  PubMed  Google Scholar 

  • Fan N, Fu N, Zhang N (2019) Progress in molecular docking. Quant Biol 7:83–89

    Article  CAS  Google Scholar 

  • Fu HW, Wang CX, Shu XL, Li YF, Wu DX, Shu QY (2007) Microsatellite analysis for revealing parentage of gamma ray-induced mutants in rice (Oryza sativa L.). Isr J Plant Sci 55:201–206

    Article  CAS  Google Scholar 

  • Fu HW, Li YF, Shu QY (2008) A revisit of mutation induction by gamma rays in rice (Oryza sativa L.): implications of microsatellite markers for quality control. Mol Breed 22(2):281–288

    Article  CAS  Google Scholar 

  • Goslings D, Meskauskiene R, Kim C, Lee KP, Nater M, Apel K (2004) Concurrent interactions of heme and FLU with Glu-tRNA reductase (HEMA1), the target of metabolic feedback inhibition of tetrapyrrole biosynthesis, in dark- and light-grown Arabidopsis plants. Plant J 40:957–967

    Article  CAS  PubMed  Google Scholar 

  • Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R (2008) Kismeth: analyzer of plant methylation states through bisulfite sequence. BMC Bioinform 9:371

    Article  CAS  Google Scholar 

  • Ilag LL, Kumar AM, Söll D (1994) Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis. Plant Cell 6:265–275

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang M, Liu YH, Li RQ, Zheng YC, Fu HW, Tan YY, Moller IM, Fan LJ, Shu QY, Huang JZ (2019) A suppressor mutation partially reverts the xantha trait via lowered methylation in the promoter of genomes uncoupled 4 in rice. Front Plant Sci 10:1003

    Article  PubMed  PubMed Central  Google Scholar 

  • Jiang M, Wu XJ, Song Y, Shen HZ, Cui HR (2020) Effects of OsMSH6 mutations on microsatellite stability and homeologous recombination in rice. Front Plant Sci 11:220

    Article  PubMed  PubMed Central  Google Scholar 

  • Jiang M, Dai S, Wang BQ, **e ZM, Li JL, Wang LY, Li S, Tan YY, Tian B, Shu QY, Huang JZ (2021) Gold nanoparticles synthesized using melatonin suppress cadmium uptake and alleviate its toxicity in rice. Environ Sci Nano 8:1042–1056

    Article  CAS  Google Scholar 

  • Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282

    CAS  PubMed  Google Scholar 

  • Kauss D, Bischof S, Steiner S, Apel K, Meskauskiene R (2012) FLU, a negative feedback regulator of tetrapyrrole biosynthesis, is physically linked to the final steps of the Mg++-branch of this pathway. FEBS Lett 586:211–216

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li RQ, Huang JZ, Zhao HJ, Fu HW, Li YF, Liu GZ, Shu QY (2014) A down-regulated epi-allele of the genomes uncoupled 4 gene generates a xantha marker trait in rice. Theor Appl Genet 127:491–501

    Google Scholar 

  • Li RQ, Jiang M, Liu YH, Zheng YC, Huang JZ, Wu JM, Shu QY (2017) The xantha marker trait is associated with altered tetrapyrrole biosynthesis and deregulated transcription of PhANGs in rice. Front Plant Sci 8:901

    Article  PubMed  PubMed Central  Google Scholar 

  • Li RQ, Jiang M, Huang JZ, Moller IM, Shu QY (2021a) Mutations of the genomes uncoupled 4 gene cause ROS accumulation and repress expression of peroxidase genes in rice. Front Plant Sci 12:682453

    Article  PubMed  PubMed Central  Google Scholar 

  • Li RQ, Jiang M, Zheng WY, Zhang HL (2021b) GUN4-mediated tetrapyrrole metabolites regulates starch biosynthesis during early seed development in rice. J Cereal Sci 101:103317

    Article  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta c (t)) method. Methods 25:402–408

    CAS  PubMed  Google Scholar 

  • Matsumoto F, Obayashi T, Sasaki-Sekimoto Y, Ohta H, Takamiya K, Masuda T (2004) Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system. Plant Physiol 135:2379–2391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mauzerall D, Granick S (1956) The occurrence and determination of d-aminolevulinic acid and porphobilinogen in urine. J Biol Chem 219:435–446

    Article  CAS  PubMed  Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meskauskiene R, Nater M, Goslings D, Kessler F, Camp R, Apel K (2001) FLU: A negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA 98:12826–12831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mochizuki N, Tanaka R, Grimm B, Masuda T, Moulin M, Smith AG, Tanaka A, Terry MJ (2010) The cell biology of tetrapyrroles: a life and death struggle. Trends Plant Sci 15:488–498

    Article  CAS  PubMed  Google Scholar 

  • Moser J, Schubert WD, Beier V, Bringemeier I, Jahn D, Heinz DW (2001) V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. EMBO J 20:6583–6590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497

    Article  CAS  Google Scholar 

  • Nagai S, Koide M, Takahashi S, Kikuta A, Aono M, Sasaki-Sekimoto OH, Takamiya K, Masuda T (2007) Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis. Plant Physiol 144:1039–1051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nogaj LA, Beale SI (2005) Physical and kinetic interactions between glutamyl-tRNA reductase and glutamate-1-semialdehyde aminotransferase of Chlamydomonas reinhardtii. J Biol Chem 280:24301–24307

    Article  CAS  PubMed  Google Scholar 

  • Pontoppidan B, Kannangara CG (1994) Purification and partial characterizationof barley glutamyl-tRNA(Glu) reductase, the enzyme that directs glutamate tochlorophyll biosynthesis. Eur J Biochem 225:529–537

    Article  CAS  PubMed  Google Scholar 

  • Porra RJ, Klein O, Wright PE (1983) Proof by 13C-NMR spectroscopy of the predominance of the C5 pathway over the Shemin pathway in chlorophyll biosynthesis in higher plants and of the formation of the methyl ester group of chlorophyll from glycine. Eur J Biochem 130:509–516

    Article  CAS  PubMed  Google Scholar 

  • Rebeiz CA, Montazer-Zouhoor A, Mayasich JM, Tripathy BC, Wu SM, Rebeiz CC, Friedmann HC (1988) Photodynamic herbicides. Recent developments and molecular basis of selectivity. Crit Rev Plant Sci 6:385–436

    Article  CAS  Google Scholar 

  • Song Y, Jiang M, Zhang HL, Li RQ (2021) Zinc oxide nanoparticles alleviate chilling stress in rice (Oryza Sativa L.) by regulating antioxidative system and chilling response transcription factors. Molecules 26(8):2196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Srivastava A, Beale SI (2005) Glutamyl-tRNA reductase of Chlorobium vibrioforme is a dissociable homodimer that contains one tightly bound heme per subunit. J Bacteriol 187:4444–4450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S et al (2013) QTL-seq: rapid map** of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183

    Article  CAS  PubMed  Google Scholar 

  • Tan YY, Fu HW, Zhao HJ, Lu S, Fu JJ, Li YF, Cui HR, Shu QY (2013) Functional molecular markers and high-resolution melting curve analysis of low phytic acid mutations for marker-assisted selection in rice. Mol Breed 31:517–528

    Article  CAS  Google Scholar 

  • Tanaka R, Tanaka A (2007) Tetrapyrrole biosynthesis in higher plants. Annu Rev Plant Biol 58:321–346

    Article  CAS  PubMed  Google Scholar 

  • The 3000 Rice Genomes Project (2014) The 3000 rice genomes project. GigaScience 3:7

    Article  CAS  Google Scholar 

  • Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tu JM, Ona I, Zhang QF, Mew TW, Khush GS, Datta SK (1998) Transgenic rice variety ‘IR72’ with Xa21 is resistance to bacterial blight. Theor Appl Genet 97:31–36

    Article  CAS  Google Scholar 

  • Vothknecht UC, Kannangara CG, Von Wettstein D (1996) Expression of catalytically active barley glutamyl tRNAGlu reductase in Escherichia coli as a fusion protein with glutathione S-transferase. Proc Natl Acad Sci USA 93:9287–9291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vothknecht UC, Kannangara CG, Von Wettstein D (1998) Barley glutamyl tRNAGlu reductase: mutations affecting haem inhibition and enzyme activity. Phytochemistry 47:513–519

    Article  CAS  PubMed  Google Scholar 

  • Wang Q, Zhu B, Chen C, Yuan Z, Guo J, Yang X, Wang S, Lv Y, Liu Q, Yang B, Sun C, Wang P, Deng X (2021) A single nucleotide substitution of GSAM gene causes massive accumulation of glutamate 1-semialdehyde and yellow leaf phenotype in rice. Rice 14:50

    Article  PubMed  PubMed Central  Google Scholar 

  • Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucl Acids Res 46:296–303

    Article  CAS  Google Scholar 

  • Wu Y, Liao W, Dawuda MM, Hu L, Yu J (2019) 5-Aminolevulinic acid (ALA) biosynthetic and metabolic pathways and its role in higher plants: a review. Plant Growth Regul 87:357–374

    Article  CAS  Google Scholar 

  • Yarra R, Sahoo L (2021) Base editing in rice: current progress, advances, limitations, and future perspectives. Plant Cell Rep 40:595–604

    Article  CAS  PubMed  Google Scholar 

  • Zeng Z, Lin T, Zhao J, Zheng T, Xu L, Wang Y, Liu L, Jiang L, Chen S, Wan J (2020) OsHemA gene, encoding glutamyl-tRNA reductase (GluTR) is essential for chlorophyll biosynthesis in rice (Oryza sativa). J Integr Agric 19:16–27

    Google Scholar 

  • Zhang HL, Huang JZ, Chen XY, Tan YY, Shu QY (2014) Competitive amplification of differentially melting amplicons facilitates efficient genoty** of photoperiod-and temperature-sensitive genic male sterility in rice. Mol Breed 34:1765–1776

    Article  CAS  Google Scholar 

  • Zhang M, Zhang F, Fang Y, Chen X, Chen Y, Zhang W, Dai H, Lin R, Lin L (2015) The non-canonical tetratricopeptide repeat (TPR) domain of fluorescent (FLU) mediates complex formation with Glutamyl-tRNA reductase. J Biol Chem 290:17559–17565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao A, Fang Y, Chen X, Zhao S, Dong W, Lin Y, Gong W, Liu L (2014) Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its stimulator protein. Proc Natl Acad Sci USA 111:6630–6635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou XS, Shen SQ, Wu DX, Sun JW, Shu QY (2006) Introduction of a xantha mutation for testing and increasing varietal purity in hybrid rice. Field Crop Res 96:71–79

    Article  Google Scholar 

Download references

Acknowledgements

We thank Prof. Huixia Shou from the College of Life Sciences, Zhejiang University for sharing the vectors (pGBKT7, pGADT7-Rec, pET30a, and pDEST15).

Funding

This study was supported by the National Nuclear Energy Exploitation Program-Nuclear Irradiation for Crop Improvement and Insect Eradication, the Fundamental Research Funds for the Central Universities (226-2022-00012), and the China Postdoctoral Science Foundation (2020M680078). IMM was supported by a travel grant from the 111 Plan project.

Author information

Authors and Affiliations

  1. National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China

    Meng Jiang, Yun-Chao Zheng, Yuan-Yuan Tan, Gang Pan, Shi-Yong Song, Jian-Zhong Huang & Qing-Yao Shu

  2. Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, Hainan, China

    Meng Jiang, Jian-Zhong Huang & Qing-Yao Shu

  3. Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310058, China

    Meng Jiang & Jian-Zhong Huang

  4. MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China

    Shang Dai

  5. College of Agronomy, Anhui Agricultural University, Hefei, 230036, China

    Rui-Qing Li

  6. Department of Molecular Biology and Genetics, Aarhus University, 4200, Slagelse, Denmark

    Ian Max Møller

Authors
  1. Meng Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shang Dai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yun-Chao Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rui-Qing Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuan-Yuan Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gang Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ian Max Møller
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shi-Yong Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jian-Zhong Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Qing-Yao Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

QYS, MJ, and JZH planned and designed the research. MJ, SD, and YCZ performed the bioinformatic analyses, and MJ, SD, RQL, YYT, and GP performed the laboratory experiments. MJ, SD, RQL, and QYS analyzed the data together. MJ finished the first draft, and IMM, SYS, JZH, and QYS edited and converted the draft into the submitted manuscript. All authors reviewed and approved the final manuscript.

Corresponding authors

Correspondence to Jian-Zhong Huang or Qing-Yao Shu.

Ethics declarations

Conflict of interest

The authors declare no conflicts of interest.

Additional information

Communicated by Yunbi Xu.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 2781 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jiang, M., Dai, S., Zheng, YC. et al. An alanine to valine mutation of glutamyl-tRNA reductase enhances 5-aminolevulinic acid synthesis in rice. Theor Appl Genet 135, 2817–2831 (2022). https://doi.org/10.1007/s00122-022-04151-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-022-04151-7

Search

Navigation