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Oscaf1, a CRM Domain Containing Protein, Influences Chloroplast

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Oscaf1, a CRM Domain Containing Protein, Influences Chloroplast International Journal of Molecular Sciences Article OsCAF1, a CRM Domain Containing Protein, Influences Chloroplast Development 1, 1, 2 1 1 1 Qiang Zhang y , Lan Shen y, Zhongwei Wang , Guanglian Hu , Deyong Ren , Jiang Hu , Li Zhu 1, Zhenyu Gao 1, Guangheng Zhang 1 , Longbiao Guo 1, Dali Zeng 1 and Qian Qian 1,* 1 State Key Laboratory of Rice Biology/China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China 2 Biotechnology Research Center, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China * Correspondence: [email protected]; Tel.: +86-571-63371418 These authors contributed equally to this study. y Received: 6 July 2019; Accepted: 3 September 2019; Published: 6 September 2019 Abstract: The chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are involved in the splicing of chloroplast gene introns. Numerous CRM domain proteins have been reported to play key roles in chloroplast development in several plant species. However, the functions of CRM domain proteins in chloroplast development in rice remain poorly understood. In the study, we generated oscaf1 albino mutants, which eventually died at the seedling stage, through the editing of OsCAF1 with two CRM domains using CRISPR/Cas9 technology. The mesophyll cells in oscaf1 mutant had decreased chloroplast numbers and damaged chloroplast structures. OsCAF1 was located in the chloroplast, and transcripts revealed high levels in green tissues. In addition, the OsCAF1 promoted the splicing of group IIA and group IIB introns, unlike orthologous proteins of AtCAF1 and ZmCAF1, which only affected the splicing of subgroup IIB introns. We also observed that the C-terminal of OsCAF1 interacts with OsCRS2, and OsCAF1–OsCRS2 complex may participate in the splicing of group IIA and group IIB introns in rice chloroplasts. OsCAF1 regulates chloroplast development by influencing the splicing of group II introns. Keywords: chloroplast RNA splicing and ribosome maturation (CRM) domain; intron splicing; chloroplast development; rice 1. Introduction Chloroplasts are important organelles in plants. A series of metabolic processes occur in chloroplasts, including photosynthesis and anabolism of compounds such as tetrapyrroles, terpenoids, lipids, amino acids, and hormones [1]. Chloroplasts are considered semi-autonomous organelles because their development is not only influenced by their own genetic material but also by fine regulation by nuclear-encoded genes [2,3]. Studies have shown that by plastid-encoded polymerases (PEPs) and nucleus-encoded polymerases (NEPs) influence the development of chloroplasts [4–6]. Chloroplast genes encode approximately 100 proteins, some of which have one or more introns that cannot be self-spliced, and the primary RNA transcription of such chloroplast genes require splicing by ribozymes potentially via chemical steps similar to spliceosome-mediated splicing in the nucleus [7–9]. In plants, based on the primary sequences, predicted structures, and splicing mechanisms, the introns of the chloroplast are mainly classified into two categories, including group I and group II [10]. Group II introns are mainly divided further into two subgroups, including subgroup IIA introns and subgroup IIB introns [11]. Arabidopsis thaliana, maize, and rice chloroplast genomes all have only 1 group I intron, and 20, 17, and 17 group II introns, respectively [8]. In plant chloroplasts, such introns have lost the Int. J. Mol. Sci. 2019, 20, 4386; doi:10.3390/ijms20184386 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2019, 20, 4386 2 of 13 capacity to self-splice in vivo and require nuclear gene-encoded proteins as co-factors to participate in splicing [8,12]. Numerous studies have shown that nuclear-encoded pentatricopeptide repeat (PPR) proteins participate in chloroplast RNA editing and splicing, which are critical for chloroplast development and function [8,13]. Currently, the large PPR protein families, including AtOTP51, ZmPPR5, OsPPR6, and OsPPR1, are considered to participate in different chloroplast group II intron splicing activities [14–18]. Previous studies have shown that the disruption of the normal functions of such PPR proteins could lead to abnormal chloroplast development, which would lead to albino seedlings or death of plants [14–18]. In addition to the PPR proteins mentioned above, chloroplast RNA splicing and ribosome maturation (CRM) domain proteins participate in the splicing of chloroplast gene introns [8]. In plants, the splicing of chloroplast introns requires splicing factors encoded by nuclear genes and the abnormal splicing of chloroplast intron will affect the development of chloroplast [14–16]. Several proteins with CRM domains have been identified as splicing co-factors, including CFM2, CFM3, CRS1, CAF1, and CAF2 [8]. Both ZmCFM2 and AtCFM2 have four CRM domains, and they participate in the splicing of ndhA and ycf3-1 subgroup IIB and group I introns. In A. thaliana, AtCFM2 potentially promotes the splicing of clpP introns [19]. CFM3 and CRS1 contain three CRM domains, and AtCRS1 and ZmCRS1 have been associated with the splicing of the atpF intron, which belongs to subgroup IIA introns [20,21]. In addition, CFM3 has been reported to be dual-localized in chloroplasts and mitochondria, and CFM3a is required for the splicing of group II introns, including ndhB, rpl16, rps16, petD, and petB introns in chloroplasts [19]. The CAF1 and CAF2 contain two CRM domains, which are required for the splicing of group IIB introns, including ndhA, ndhB, petB, petD, rpl16, rps16, trnG, and ycf3-1 in maize and A. thaliana [11,21]. In A. thaliana, AtCAF2 potentially promotes the splicing of rpoC1 and ClpP introns that are absent in the maize chloroplast genome [21]. In addition, CAF1 and CAF2 could interact with CRS2, forming the CRS2–CAF1 and CRS2–CAF2 complexes, which participate in the splicing of chloroplast group II introns and the regulation of chloroplast development in maize [22]. Previous studies have shown that there are 14 proteins that contain one or more CRM domains in rice [8]. To date, researchers have only studied the functions of OsCRS1 and OsCFM3, which contain three CRM domains. The studies revealed that oscrs1 mutants exhibited albino leaf phenotypes in rice [23]. In addition, OsCRS1 has been reported to participate in the splicing of ndhA, ndhB, petD, ycf3-1, and trnL introns and it could influence the expression of PEP-dependent genes such as psaA and psbA [23]. Furthermore, oscfm3 T-DNA insertion mutants exhibited albino seedling phenotypes; however, the OsCFM3 participates in the intron splicing of ndhB, petD, rps16, and rpl16 in rice [19]. The functions of other CRM domain proteins have hardly been reported in rice. Previous studies have shown that homologous CAF1 plays important roles in chloroplast development in A. thaliana and Zea mays L. In rice, the function of OsCAF1 remains unknown and investigating its function would enhance our understanding of mechanisms of chloroplast development. In this study, we investigated the function of OsCAF1 in rice chloroplast development, and oscaf1 mutants were obtained using the CRISPR-Cas9 system. The results of our study revealed that oscaf1 mutants exhibited albino seedlings phenotype along with a damaged chloroplast structure. In rice, chloroplast development is regulated by the expression of PEP-dependent genes, which could be affected by OsCAF1. In addition, we observed that the leaves of oscaf1 mutants accumulated higher hydrogen peroxide (H2O2) contents. In addition, OsCAF1 could interact with the OsCRS2 via C-terminal, and then form an OsCAF1–OsCRS2 complex that regulates the splicing of chloroplast gene introns. Chloroplast RNA splicing analysis showed that OsCAF1 influenced the splicing of both chloroplast subgroup IIA and subgroup IIB introns, which is different from the orthologous proteins of AtCAF1 and ZmCAF1, which both influence the splicing of chloroplast subgroup IIB introns. The results of the present study reveal the functions of OsCAF1 in the regulation of rice chloroplast development. Int. J. Mol. Sci. 2019, 20, 4386 3 of 13 Int.2.Results J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 3 of 13 2.1. Knockout Knockout of OsCAF1 Produced the Albino Seedling Phenotype According to a previous study, the orthologortholog of ZmCAF1 inin ricerice waswas Os01g0495900Os01g0495900, which was named OsCAF1, and the function of OsCAF1 has not been determined to date [8]. [8]. We observed that the cDNA cDNA of of OsCAF1OsCAF1 hadhad a a2106-bp 2106-bp nucleotide nucleotide and and encoded encoded 701 701 amino amino acids acids (aa). (aa). To determine To determine the functionthe function of OsCAF1 of OsCAF1 in inrice rice chloroplast chloroplast development, development, oscaf1oscaf1 mutantsmutants were were generated generated using using the CRISPR/Cas9CRISPR/Cas9 system (Figure 11A,B),A,B), andand 2626 transgenictransgenic plantsplants werewere obtainedobtained inin thethe TT0 generation.generation. Sequencing and phenotypic analysis revealed that oscaf1 homozygous mutants exhibited the albino phenotype inin thethe ricerice seedingseeding stage stage (Figure (Figure1C,D), 1C,D), and an thend then died died after after the the three three leaves leaves stage. stage. In bothIn both of of#3 #3 and and #4 mutants,#4 mutants, a premature a premature stop stop codon codon was createdwas created by a frame by a shiftframe in shift the coding in the regioncoding of regionOsCAF1 of. OsCAF1However,. However, the OsCAF1 the/oscaf1 OsCAF1/oscaf1heterozygous
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