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Proteomic and functional analysis of soybean chlorophyll-deficient mutant cd1 and the underlying gene encoding the CHLI subunit of Mg-chelatase

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Abstract

Sufficient chlorophyll biosynthesis is vital for the growth of photoautotrophic plants. Mg-chelatase, consisting of three subunits (CHLI, CHLD, and CHLH), catalyzes the insertion of Mg2+ into protoporphyrin IX, which is the rate-limiting step of chlorophyll biosynthesis. A chlorophyll-deficient mutant (cd1) was previously identified by phenotype. This mutant shows a chlorina phenotype, abnormal chloroplasts, and lower chlorophyll content, plant height, and seed yield than the WT (Nannong 86-4). In this study, map-based cloning of cd1 revealed that a missense mutation (G1709A) was present in GmCHLI1b, leading to an amino acid substitution (D278N) in the Arg-finger domain. Yeast two-hybrid assays indicated that this substitution weakened the interaction between Gmcd1 and GmCHLI1a/b. In addition, GmCHLI1b was not a target protein of GmTrxF1/2 or GmNTRC1/2 in the Y2H system but could interact with them in a bimolecular fluorescence complementation (BiFC) assay. A proteomic analysis of leaf soluble proteins identified 31 differentially accumulated proteins, mainly involved in photosynthesis, carbon fixation in photosynthetic organisms, and carbohydrate/energy and amino acid/protein metabolism. These results indicated that cd1 possesses weaker photosynthesis, respiration and protein metabolism and that its leaf redox homeostasis is disrupted. Global transcriptome analysis of chlorophyll biosynthesis and RT-PCR demonstrated a transcriptional downregulation of photosynthesis-associated genes in cd1 during the diurnal rhythm. This study provides insights into the mechanisms of molecular regulation in the cd1 mutant and adds to the knowledge of the biological and biochemical functions of GmCHLIs in soybean.

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References

  • Albrecht V, Ingenfeld A, Apel K (2006) Characterization of the snowy cotyledon 1 mutant of Arabidopsis thaliana: the impact of chloroplast elongation factor G on chloroplast development and plant vitality. Plant Mol Biol 60:507–518

    Article  PubMed  CAS  Google Scholar 

  • CampbellBW, ManiD, CurtinSJ, SlatteryRA, MichnoJM, OrtDR, SchausPJ, PalmerRG, OrfJH, StuparRM (2014) Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (Bethesda, Md) 5

  • Chen X, Pu H, Fang Y, Wang X, Zhao S, Lin Y, Zhang M, Dai H-E, Gong W, Liu L (2015) Crystal structure of the catalytic subunit of magnesium chelatase. Nat Plants 1:15125

    Article  PubMed  CAS  Google Scholar 

  • Davison PA, Schubert HL, Reid JD, Iorg CD, Heroux A, Hill CP, Hunter CN (2005) Structural and biochemical characterization of Gun4 suggests a mechanism for its role in chlorophyll biosynthesis. Biochemistry 44:7603–7612

    Article  PubMed  CAS  Google Scholar 

  • Du SY, Zhang XF, Lu Z, **n Q, Wu Z, Jiang T, Lu Y, Wang XF, Zhang DP (2012) Roles of the different components of magnesium chelatase in abscisic acid signal transduction. Plant Mol Biol 80:519–537

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fodje MN, Hansson AM, Olsen JG, Gough S, Willows RD (2001) Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. J Mol Biol 311:111–122

    Article  PubMed  CAS  Google Scholar 

  • Guan R, Qu Y, Guo Y, Yu L, Liu Y, Jiang J, Chen J, Ren Y, Liu G, Tian L, ** L, Liu Z, Hong H, Chang R, Gilliham M, Qiu L (2014) Salinity tolerance in soybean is modulated by natural variation in GmSALT3. Plant J 80:937–950

    Article  PubMed  CAS  Google Scholar 

  • Hansson A, Hansson M (1999) Molecular basis for semidominance of missense mutations in the XANTHA-H (42-kDa) subunit of magnesium chelatase. Proc Natl Acad Sci U S A 96:1744–1749

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hansson A, Willows RD, Roberts TH, Hansson M (2002) Three semidominant barley mutants with single amino acid substitutions in the smallest magnesium chelatase subunit form defective AAA+ hexamers. Proc Natl Acad Sci U S A 99:13944–13949

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hortensteiner S (2013) Update on the biochemistry of chlorophyll breakdown. Plant Mol Biol 82:505–517

    Article  PubMed  CAS  Google Scholar 

  • Huang YS, Li HM (2009) Arabidopsis CHLI2 can substitute for CHLI1. Plant Physiol 150:636–645

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ikegami A, Yoshimura N, Motohashi K, Takahashi S, Romano PG, Hisabori T, Takamiya K, Masuda T (2007) The CHLI1 subunit of Arabidopsis thaliana magnesium chelatase is a target protein of the chloroplast thioredoxin. J Biol Chem 282:19282–19291

    Article  PubMed  CAS  Google Scholar 

  • Karata K, Inagawa T, Wilkinson AJ, Tatsuta T, Ogura T (1999) Dissecting the role of a conserved motif (the second region of homology) in the AAA family of ATPases. J Biol Chem 274:26225–26232

    Article  PubMed  CAS  Google Scholar 

  • Kato KK, Palmer RG (2004) Duplicate chlorophyll-deficient loci in soybean. Genome 47:190–198

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi K, Mochizuki N, Yoshimura N, Motohashi K, Hisabori T, Masuda T (2008) Functional analysis of Arabidopsis thaliana isoforms of the Mg-chelatase CHLI subunit. Photochem Photobiol Sci 7:1188–1195

    Article  PubMed  CAS  Google Scholar 

  • Larkin RM, Alonso JM, Ecker JR, Chory J (2003) GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299:902–906

    Article  PubMed  CAS  Google Scholar 

  • Li HM, Chiu CC (2010) Protein transport into chloroplasts. Annu Rev Plant Biol 61:157–180

    Article  PubMed  CAS  Google Scholar 

  • Li Q, Fang C, Duan Z, Liu Y, Qin H, Zhang J, Sun P, Li W, Wang G, Tian Z (2016) Functional conservation and divergence of GmCHLI genes in polyploid soybean. Plant J 88:584–596

    Article  PubMed  CAS  Google Scholar 

  • Lichtenthaler HK (1987) Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. Methods Enzymol 148:350–382

    Article  CAS  Google Scholar 

  • Liu X, Yu W, Wang G, Cao F, Cai J, Wang H (2016) Comparative proteomic and physiological analysis reveals the variation mechanisms of leaf coloration and carbon fixation in a xantha mutant of Ginkgo biloba L. Int J Mol Sci 17

  • Lundqvist J, Elmlund H, Wulff RP, Berglund L, Elmlund D, Emanuelsson C, Hebert H, Willows RD, Hansson M, Lindahl M, Al-Karadaghi S (2010) ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase. Structure 18:354–365

    Article  PubMed  CAS  Google Scholar 

  • Luo T, Fan T, Liu Y, Rothbart M, Yu J, Zhou S, Grimm B, Luo M (2012) Thioredoxin redox regulates ATPase activity of magnesium chelatase CHLI subunit and modulates redox-mediated signaling in tetrapyrrole biosynthesis and homeostasis of reactive oxygen species in pea plants. Plant Physiol 159:118–130

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Masuda T (2008) Recent overview of the Mg branch of the tetrapyrrole biosynthesis leading to chlorophylls. Photosynth Res 96:121–143

    Article  PubMed  CAS  Google Scholar 

  • Palmer RG, Xu M (2008) Positioning 3 qualitative trait loci on soybean molecular linkage group E. J Hered 99:674–678

    Article  PubMed  CAS  Google Scholar 

  • Perez-Ruiz JM, Guinea M, Puerto-Galan L, Cejudo FJ (2014) NADPH thioredoxin reductase C is involved in redox regulation of the Mg-chelatase I subunit in Arabidopsis thaliana chloroplasts. Mol Plant 7:1252–1255

    Article  PubMed  CAS  Google Scholar 

  • Reed S, Atkinson T, Gorecki C, Espinosa K, Przybylski S, Goggi A, Palmer R, Sandhu D (2014) Candidate gene identification for a lethal chlorophyll-deficient mutant in soybean. Agronomy 4:462–469

    Article  CAS  Google Scholar 

  • Reinbothe C, El Bakkouri M, Buhr F, Muraki N, Nomata J, Kurisu G, Fujita Y, Reinbothe S (2010) Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction. Trends Plant Sci 15:614–624

    Article  PubMed  CAS  Google Scholar 

  • Richter AS, Peter E, Rothbart M, Schlicke H, Toivola J, Rintamäki E, Grimm B (2013) Posttranslational influence of NADPH-dependent thioredoxin reductase C on enzymes in tetrapyrrole synthesis. Plant Physiol 162:63–73

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rissler HM, Collakova E, DellaPenna D, Whelan J, Pogson BJ (2002) Chlorophyll biosynthesis. Expression of a second chl I gene of magnesium chelatase in Arabidopsis supports only limited chlorophyll synthesis. Plant Physiol 128:770–779

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sawers RJ, Viney J, Farmer PR, Bussey RR, Olsefski G, Anufrikova K, Hunter CN, Brutnell TP (2006) The maize Oil yellow1 (Oy1) gene encodes the I subunit of magnesium chelatase. Plant Mol Biol 60:95–106

    Article  PubMed  CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Article  PubMed  CAS  Google Scholar 

  • Shoemaker RC, Schlueter J, Doyle JJ (2006) Paleopolyploidy and gene duplication in soybean and other legumes. Curr Opin Plant Biol 9:104–109

    Article  PubMed  CAS  Google Scholar 

  • Soldatova O, Apchelimov A, Radukina N, Ezhova T, Shestakov S, Ziemann V, Hedtke B, Grimm B (2005) An Arabidopsis mutant that is resistant to the protoporphyrinogen oxidase inhibitor acifluorfen shows regulatory changes in tetrapyrrole biosynthesis. Mol Gen Genomics 273:311–318

    Article  CAS  Google Scholar 

  • Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang E-Y, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50:1950–1960

    Article  CAS  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  PubMed  CAS  Google Scholar 

  • Tanaka A, Tanaka R (2006) Chlorophyll metabolism. Curr Opin Plant Biol 9:248–255

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Tian Z, Wang X, Lee R, Li Y, Specht JE, Nelson RL, McClean PE, Qiu L, Ma J (2010) Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci U S A 107:8563–8568

    Article  PubMed  PubMed Central  Google Scholar 

  • WaadtR, KudlaJ (2008) In planta visualization of protein interactions using bimolecular fluorescence complementation (BiFC) [J]. CSH Protocal, pdb prot4995

  • Wang P, Grimm B (2015) Organization of chlorophyll biosynthesis and insertion of chlorophyll into the chlorophyll-binding proteins in chloroplasts. Photosynth Res 126:189–202

    Article  PubMed  CAS  Google Scholar 

  • **a Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Anai T, Sato S, Yamazaki T, Lu S, Wu H, Tabata S, Harada K (2012) Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A 109:E2155–E2164

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu M, Palmer RG (2005) Molecular map** of k2Mdh1-ny20, an unstable chromosomal region in soybean [Glycine max (L.) Merr.]. Theor Appl Genet 111:1457–1465

    Article  PubMed  CAS  Google Scholar 

  • Yoo SD, Cho YH, Sheen J (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2:1565–1572

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Li J, Yoo JH, Yoo SC, Cho SH, Koh HJ, Seo HS, Paek NC (2006) Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development. Plant Mol Biol 62:325–337

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Liu L, Cai M, Zhu S, Zhao J, Zheng T, Xu X, Zeng Z, Niu J, Jiang L, Chen S, Wan J (2015) A point mutation of magnesium chelatase OsCHLI gene dampens the interaction between CHLI and CHLD subunits in rice. Plant Mol Biol Report 33:1975–1987

    Article  CAS  Google Scholar 

  • Zhang H, Zhang D, Han S, Zhang X, Yu D (2011) Identification and gene map** of a soybean chlorophyll-deficient mutant. Plant Breed 130:133–138

    Article  CAS  Google Scholar 

  • Zheng R, Yue S, Xu X, Liu J, Xu Q, Wang X, Han L, Yu D (2012) Proteome analysis of the wild and YX-1 male sterile mutant anthers of wolfberry (Lycium barbarum L.). PLoS One 7:e41861

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zou JJ (2003) Association of the yellow leaf (y10) mutant to soybean chromosome 3. J Hered 94:352–355

    Article  PubMed  CAS  Google Scholar 

Download references

Funding

This work was supported in part by the Ministry of Science and Technology (2016YFD0100304, 2017YFE0111000), Key Transgenic Breeding Program of China (2016ZX08004-003), National Natural Science Foundation of China (31701453,31671715), Fundamental Research Funds for the Central Universities (Y0201600116), and Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP).

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Correspondence to Deyue Yu.

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Du, H., Qi, M., Cui, X. et al. Proteomic and functional analysis of soybean chlorophyll-deficient mutant cd1 and the underlying gene encoding the CHLI subunit of Mg-chelatase. Mol Breeding 38, 71 (2018). https://doi.org/10.1007/s11032-018-0819-9

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