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RLIN1, Encoding a Putative Coproporphyrinogen III Oxidase, Is Involved in Lesion Initiation in Rice

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RLIN1, Encoding a Putative Coproporphyrinogen III Oxidase, Is Involved in Lesion Initiation in Rice Available online at www.sciencedirect.com Journal of Genetics and Genomics 38 (2011) 29e37 www.jgenetgenomics.org RLIN1, encoding a putative coproporphyrinogen III oxidase, is involved in lesion initiation in rice Changhui Sun a,b,d,1, Linchuan Liu b,c,1, Jiuyou Tang b, Aihong Lin b,c, Fantao Zhang b,d, Jun Fang b, Genfa Zhang a,*, Chengcai Chu a,b,c,* a Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China b The State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China c Graduate School of the Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China d Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China Received 11 October 2010; revised 17 October 2010; accepted 20 October 2010 Abstract Lesion mimic is necrotic lesions on plant leaf or stem in the absence of pathogenic infection, and its exact biological mechanism is varied. By a large-scale screening of our T-DNA mutant population, we identified a mutant rice lesion initiation 1 (rlin1), which was controlled by a single nuclear recessive gene. Map-based cloning revealed that RLIN1 encoded a putative coproporphyrinogen III oxidase in tetrapyrrole biosynthesis pathway. Sequencing results showed that a G to T substitution occurred in the second exon of RLIN1 and led to a missense mutation from Asp to Tyr. Ectopic expression of RLIN1 could rescue rlin1 lesion mimic phenotype. Histochemical analysis demonstrated that lesion formation in rlin1 was light-dependent accompanied by reactive oxygen species accumulated. These results suggest that tetrapyrrole participates in lesion formation in rice. Keywords: Rice; Map-based cloning; Lesion mimic; Coproporphyrinogen III oxidase; Tetrapyrrole 1. Introduction pathway is very complex and fine regulated (Mock and Grimm, 1997; Grimm, 1998). In higher plant, there are four Tetrapyrrole has been studied over several decades as well- kinds of tetrapyrroles: chlorophyll, heme, siroheme, and known photosensitizers (Tanaka and Tanaka, 2007; Hirashima phytochromobilin (Tanaka and Tanaka, 2007). All the classes et al., 2009). It has been found that tetrapyrroles play impor- of tetrapyrroles share the same pathway from glutamate to tant roles in many biological processes such as light harvest- uroporphyrinogen III. Subsequently, uroporphyrinogen III is ing, photophosphorylation, removal of reactive oxygen converted to protoporphyrin IX in three steps catalyzed by species, oxygen transport etc. (Grimm, 1998; Ishikawa et al., three distinct enzymes respectively: uroporphyrinogen decar- 2001). It has been shown that the tetrapyrrole biosynthesis boxylase (UROD), coproporphyrinogen III oxidase (CPOX) and protoporpyrinogen IX oxidase (PPOX), all these three Abbreviations: rlin1, rice lesion initiation 1; UROD, uroporphyrinogen steps are shared by chlorophyll, heme, and phytochromobilin decarboxylase; CPOX, coproporphyrinogen III oxidase; PPOX, proto- synthesis (Tanaka and Tanaka, 2007), the other remaining porpyrinogen IX oxidase. steps are categorized into the siroheme branch (Tanaka and * Corresponding authors. Tanaka, 2007)(Fig. 1). E-mail addresses: [email protected] (G. Zhang), [email protected] (C. Chu). Previous reports have demonstrated that lesion mimic can be 1 These authors contributed equally to this work. induced by several intermediate molecules of tetrapyrrole 1673-8527/$ - see front matter Copyright Ó 2011, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved. doi:10.1016/j.jcg.2010.12.001 30 C. Sun et al. / Journal of Genetics and Genomics 38 (2011) 29e37 Here, we identified a lesion initiation mutant rlin1, which presented a lesion mimic phenotype, affected by a single recessive nuclear gene in rice. RLIN1 gene was mapped on the long arm of chromosome 4 between two markers STS3 and STS4 in an 85 kb region, among the 13 ORFs in this region, LOC_Os04g52130 encoding a putative CPOX, substituted one base of G to T in the second exon, causing a missense muta- tion from Asp to Tyr. The lesion phenotype of rlin1 could be rescued by overexpression of LOC_Os04g52130. Taken together, we show that RLIN1 which may be a tetrapyrrole biosynthesis gene is involved in lesion formation in rice. 2. Materials and methods 2.1. Rice materials The spontaneous lesion formation mutant rlin1 was first identified from a T-DNA insertion population which was generated in our laboratory (Ma et al., 2009), but the pheno- type of rlin1 was not co-segregated with T-DNA, to this end, the rlin1 line without T-DNA insertion was isolated for progenies for further analysis. F1 and F2 population from a cross between rlin1 and Minghui 63 (Oryza sativa ssp. Fig. 1. Tetrapyrrole biosynthesis pathway. The four classes of tetrapyrroles, indica) were used to determine whether rlin1 was controlled chlorophyll, heme, phytochromobilin, and siroheme are shown in bold. CPOX by single nuclear recessive gene. This F2 population was also represents coproporphyrinogen III oxidase; PPOX indicates protoporpyrinogen used to map the gene RLIN1. All the plants were grown in IX oxidase; UROD indicates uroporphyrinogen decarboxylase. a paddy field at the Changping experimental station of Insti- tute of Genetics and Developmental Biology in Beijing, China. metabolism. So far, a number of genes responsible for lesion initiation involved in tetrapyrrole metabolism have been iso- 2.2. DNA extraction and PCR lated in higher plants (Hirashima et al., 2009). Repressing the expression levels of UROD, CPOX, and PPOX can lead to Genomic DNA was extracted from leaves following the a light-dependent lesion formation in tobacco and Arabidopsis protocol described by Edwards et al. (1991). The PCR mixture m m m  respectively (Kruse et al., 1995; Mock and Grimm, 1997; Mock was mixed with 1 L DNA (10 ng/ L), 2 L10 buffer, m m m m et al., 1997, 1998, 1999; Molina et al., 1999; Ishikawa et al., 0.4 L primers (10 mol/ L), 0.4 L dNTP (10 mmol/L), m m m 2001). The CPOX-deficiency mutant lin2 shows a lesion 0.3 L Taq (5 U/ L), and 15.9 L ddH2O. PCR for mapping was performed as the following: pre-denaturation at 95 C for formation phenotype on both leaves and siliques in Arabidopsis (Ishikawa et al., 2001). Les22, encoding a UROD, appears to 5 min followed by 31 cycles of denaturation at 95 C for 30 s; annealing at 50e55 C for 30 s; extension at 72 C for 40 s; participate in natural porphyria in maize (Hu et al., 1998). Besides UROD, CPOX and PPOX, some other molecules of with a final extension at 72 C for 20 min. The PCR products tetrapyrrole metabolism are also involved in lesion formation. were separated on 4.0% agarose gels, stained with ethidium Reduction of the plastidic ferrochelatase by antisense RNA bromide and photographed. expression leads to leaf necrosis in transgenic tobacco plants (Papenbrock et al., 2001). Accumulated pheophorbide a can 2.3. Molecular markers cause light-independent cell death along with chlorophyll breakdown (Hirashima et al., 2009); Lls1 encoding a pheo- In our lab, there were totally 290 SSR (simple sequence phorbide a oxygenase involves in lesion initiation in maize repeats) and STS (sequence-tagged site markers) markers (Yang et al., 2004). In Arabidopsis, two chlorophyll break- distributed on 12 chromosomes of rice. Among them, we down related genes, Accelerated cell death 1 (Acd1) and obtained 119 SSR and STS markers showing polymorphisms Accelerated cell death 2 (Acd2) induce lesions when they are between Zhonghua 11 and Minghui 63 for linkage analysis. absent, respectively (Mach et al., 2001; Tanaka et al., 2003; SSR were obtained in microsatellite sequences database Yang et al., 2004; Ishikawa, 2005). Taken together, all these (http://www.gramene.org/microsat). The new STS markers results suggest that lesion formation and tetrapyrrole biosyn- were designed based on the different DNA sequences between thesis are closely related, but the biological mechanism of Nipponbare (Oryza sativa ssp. japonica) and 9311 (O. sativa lesion formation which is caused by the process of tetrapyrrole ssp. indica)(Tong et al., 2009). All primers were designed metabolism is still unknown. using Primer Premier 5.0 (http://www.premierbiosoft.com). C. Sun et al. / Journal of Genetics and Genomics 38 (2011) 29e37 31 2.4. Mapping and linkage map TritonX-100, pH 3.8) at 28 C for 8 h. After that, all the seedlings were cleared in boiling ethanol (95%) at 28 C for Two DNA pools were constructed from F2 mapping pop- 20 min, then destained in ethanol (95%) overnight at 28 Cto ulation; one was mixed with 22 individuals with the lesion bleach the chlorophyll before photographing. mimic phenotype of rlin1, and the other contained 22 individ- uals with wild-type phenotype. The first DNA pool was used to 2.9. RNA extraction and quantitative RT-PCR screen the markers linkage to the gene RLIN1, the second DNA pool was used to confirm the results. All the markers covering Total RNA was extracted and quantitative RT-PCR was per- the 12 chromosomes of rice were screened in Zhonghua 11 and formed with Bio-Rad CFX96 Real-time System following the Minghui 63, and then additional 836 individuals with rlin1 protocol as described previously (Yang et al., 2009). The rice phenotype were used for fine mapping. The linkage map was Actin gene was used as an internal control in quantitative RT-PCR constructed based on the segregation data. analysis, the primer pairs were 50-ACATCGCCCTGGACTAT- GACCA-30 and 50-GTCGTACTCAGCCTTGGCAAT-30,the 2.5. Gene annotation and sequences analysis primers for quantitative RT-PCR analysis of RLIN1 expression were 50-ATCATACACCTGAAGAGGGAACT-30 and 50-AGG- The 85 kb region was analyzed in the rice genome automated AAAGCTAACAAACGATTGGA-30.
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