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Yang YZ, Liu XY, Gao S, Zhang SG, Tan BC. PPR21 is involved in the splicing of nad2 introns via interacting with PPR-SMR1 and SPR2 and is essential to maize seed development. J Genet Genomics 2024:S1673-8527(24)00233-9. [PMID: 39241862 DOI: 10.1016/j.jgg.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/30/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
Pentatricopeptide repeat (PPR) proteins are a large group of eukaryote-specific RNA-binding proteins that play pivotal roles in plant organelle gene expression. Here, we report the function of PPR21 in mitochondrial intron splicing and its role in maize kernel development. PPR21 is a typical P-type PPR protein targeted to mitochondria. The ppr21 mutants are arrested in embryogenesis and endosperm development, leading to embryo lethality. Null mutations of PPR21 reduce the splicing efficiency of nad2 intron 1, 2, and 4 and impair the assembly and activity of mitochondrial complex I. Previous studies show that the P-type PPR protein EMP12 is required for the splicing of identical introns. However, our protein interaction analyses reveal that PPR21 does not interact with EMP12. Instead, both PPR21 and EMP12 interact with the small MutS-related (SMR) domain-containing PPR protein 1 (PPR-SMR1) and the short P-type PPR protein 2 (SPR2). PPR-SMR1 interacts with SPR2, and both proteins are required for the splicing of many introns in mitochondria, including nad2 intron 1, 2, and 4. These results suggest that a PPR21-(PPR-SMR1/SPR2)-EMP12 complex is involved in the splicing of nad2 introns in maize mitochondria.
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Affiliation(s)
- Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
| | - Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Song Gao
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Shu-Guang Zhang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
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2
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Gao H, Wu G, Wu F, Zhou X, Zhou Y, Xu K, Li Y, Zhang W, Zhao K, Jing Y, Feng C, Wang N, Li H. Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:1442. [PMID: 38891251 PMCID: PMC11174663 DOI: 10.3390/plants13111442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.
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Affiliation(s)
- Hongtao Gao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Guanji Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Feifei Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Xunjun Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Yonggang Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Keheng Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Yaxin Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Kuan Zhao
- Changchun Academy of Agricultural Science, Changchun 130118, China
| | - Yan Jing
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Chen Feng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Nan Wang
- Changchun Academy of Agricultural Science, Changchun 130118, China
| | - Haiyan Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
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3
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Lin Y, Yang H, Liu H, Lu X, Cao H, Li B, Chang Y, Guo Z, Ding D, Hu Y, Xue Y, Liu Z, Tang J. A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1269-1281. [PMID: 38073308 PMCID: PMC11022799 DOI: 10.1111/pbi.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/31/2023] [Accepted: 11/26/2023] [Indexed: 04/18/2024]
Abstract
A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.
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Affiliation(s)
- Yanan Lin
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Huili Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Hongmei Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiuyuan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Haofei Cao
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Bing Li
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yongyuan Chang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhanyong Guo
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yanmin Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zonghua Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, College of AgronomyHenan Agricultural UniversityZhengzhouChina
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Zang J, Zhang T, Zhang Z, Liu J, Chen H. DEFECTIVE KERNEL 56 functions in mitochondrial RNA editing and maize seed development. PLANT PHYSIOLOGY 2024; 194:1593-1610. [PMID: 37956067 DOI: 10.1093/plphys/kiad598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Proper seed development is essential for achieving grain production, successful seed germination, and seedling establishment in maize (Zea mays). In the past few decades, pentatricopeptide repeat (PPR) proteins have been proven to play an essential role in regulating the development of maize kernels through posttranscriptional RNA modification of mitochondrial genes. However, the underlying mechanisms remain largely unknown. Here, we characterized a mutant of DEFECTIVE KERNEL 56 (DEK56) with defective kernels that exhibited arrested development of both the embryo and endosperm. Accordingly, we isolated DEK56 through a map-based cloning strategy and found that it encoded an E subgroup PPR protein located in the mitochondria. Dysfunction of DEK56 resulted in altered cytidine (C)-to-uridine (U) editing efficiency at 48 editing sites across 21 mitochondrial transcripts. Notably, the editing efficiency of the maturase-related (matR)-1124 site was substantially reduced or abolished in the dek56 mutant. Furthermore, we found that the splicing efficiency of NADH dehydrogenase subunit 4 (nad4) Introns 1 and 3 was substantially reduced in dek56 kernels, which might be a consequence of the defective MatR function. Through a protein-protein interaction test, we hypothesized that DEK56 carries out its function by recruiting the PPR-DYW protein PPR motif, coiled-coil, and DYW domain-containing protein 1 (PCW1). This interaction is facilitated by Multiple Organellar RNA Editing Factors (ZmMORFs) and Glutamine-Rich Protein 23 (ZmGRP23). Based on these findings, we developed a working model of PPR-mediated mitochondrial processing that plays an essential role in the development of maize kernels. The present study will further broaden our understanding of PPR-mediated seed development and provide a theoretical basis for maize improvement.
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Affiliation(s)
- Jie Zang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tengfei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100864, China
| | - Zhaogui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huabang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Li X, Jiang Y. Research Progress of Group II Intron Splicing Factors in Land Plant Mitochondria. Genes (Basel) 2024; 15:176. [PMID: 38397166 PMCID: PMC10887915 DOI: 10.3390/genes15020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondria are important organelles that provide energy for the life of cells. Group II introns are usually found in the mitochondrial genes of land plants. Correct splicing of group II introns is critical to mitochondrial gene expression, mitochondrial biological function, and plant growth and development. Ancestral group II introns are self-splicing ribozymes that can catalyze their own removal from pre-RNAs, while group II introns in land plant mitochondria went through degenerations in RNA structures, and thus they lost the ability to self-splice. Instead, splicing of these introns in the mitochondria of land plants is promoted by nuclear- and mitochondrial-encoded proteins. Many proteins involved in mitochondrial group II intron splicing have been characterized in land plants to date. Here, we present a summary of research progress on mitochondrial group II intron splicing in land plants, with a major focus on protein splicing factors and their probable functions on the splicing of mitochondrial group II introns.
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Affiliation(s)
| | - Yueshui Jiang
- School of Life Sciences, Qufu Normal University, Qufu 273165, China;
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Wang H, Yan X, Du Q, Yan P, Xi J, Meng X, Li X, Liu H, Liu G, Fu Z, Tang J, Li WX. Maize Dek407 Encodes the Nitrate Transporter 1.5 and Is Required for Kernel Development. Int J Mol Sci 2023; 24:17471. [PMID: 38139299 PMCID: PMC10743814 DOI: 10.3390/ijms242417471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The kernel serves as the storage organ and harvestable component of maize, and it plays a crucial role in determining crop yield and quality. Understanding the molecular and genetic mechanisms of kernel development is of considerable importance for maize production. In this study, we obtained a mutant, which we designated defective kernel 407 (dek407), through ethyl methanesulfonate mutagenesis. The dek407 mutant exhibited reduced kernel size and kernel weight, as well as delayed grain filling compared with those of the wild type. Positional cloning and an allelism test revealed that Dek407 encodes a nitrate transporter 1/peptide transporter family (NPF) protein and is the allele of miniature 2 (mn2) that was responsible for a poorly filled defective kernel phenotype. A transcriptome analysis of the developing kernels showed that the mutation of Dek407 altered the expression of phytohormone-related genes, especially those genes associated with indole-3-acetic acid synthesis and signaling. Phytohormone measurements and analysis indicated that the endogenous indole-3-acetic acid content was significantly reduced by 66% in the dek407 kernels, which may be the primary cause of the defective phenotype. We further demonstrated that natural variation in Dek407 is associated with kernel weight and kernel size. Therefore, Dek407 is a potential target gene for improvement of maize yield.
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Affiliation(s)
- Hongqiu Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiaolan Yan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Qingguo Du
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pengshuai Yan
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Jinjin Xi
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiaoruo Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xuguang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Huijian Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Guoqin Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Zhongjun Fu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Wen-Xue Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Lan J, Lin Q, Zhou C, Liu X, Miao R, Ma T, Chen Y, Mou C, Jing R, Feng M, Nguyen T, Ren Y, Cheng Z, Zhang X, Liu S, Jiang L, Wan J. Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36897026 DOI: 10.1111/jipb.13477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/07/2023] [Indexed: 05/09/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.
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Affiliation(s)
- Jie Lan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunlei Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Miao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaping Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruonan Jing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Miao Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Thanhliem Nguyen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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8
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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9
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Yang H, Wang Y, Tian Y, Teng X, Lv Z, Lei J, Duan E, Dong H, Yang X, Zhang Y, Sun Y, Chen X, Bao X, Chen R, Gu C, Zhang Y, Jiang X, Ma W, Zhang P, Ji Y, Zhang Y, Wang Y, Wan J. Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:755-771. [PMID: 36333887 DOI: 10.1111/jipb.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Most of the reported P-type pentatricopeptide repeat (PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and their underlying mechanism remains largely unknown. Here, we report a rice floury endosperm22 (flo22) mutant with delayed amyloplast development in endosperm cells. Map-based cloning and complementation tests demonstrated that FLO22 encodes a mitochondrion-localized P-type PPR protein. Mutation of FLO22 resulting in defective trans-splicing of mitochondrial nad1 intron 1 and perhaps causing instability of mature transcripts affected assembly and activity of complex Ⅰ, and mitochondrial morphology and function. RNA-seq analysis showed that expression levels of many genes involved in starch and sucrose metabolism were significantly down-regulated in the flo22 mutant compared with the wild type, whereas genes related to oxidative phosphorylation and the tricarboxylic acid cycle were significantly up-regulated. In addition to involvement in splicing as a P-type PPR protein, we found that FLO22 interacted with DYW3, a DYW-type PPR protein, and they may function synergistically in mitochondrial RNA editing. The present work indicated that FLO22 plays an important role in endosperm development and plant growth by participating in nad1 maturation and multi-site editing of mitochondrial messager RNA.
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Affiliation(s)
- Hang Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zehui Lv
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Lei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinglun Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoli Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuhao Bao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuanwei Gu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yipeng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenyu Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengcheng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Ji
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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10
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Wang C, Li H, Long Y, Dong Z, Wang J, Liu C, Wei X, Wan X. A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize. Int J Mol Sci 2023; 24:1025. [PMID: 36674545 PMCID: PMC9865405 DOI: 10.3390/ijms24021025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize.
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Affiliation(s)
- Cheng Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yan Long
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Jianhui Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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11
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Jung L, Schleicher S, Alsaied Taha F, Takenaka M, Binder S. The MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4) is essential for the accumulation of dicistronic rpl5-cob mRNAs in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:375-386. [PMID: 36468791 DOI: 10.1111/tpj.16053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis thaliana genome harbors more than 450 nuclear genes encoding pentatricopeptide repeat (PPR) proteins that operate in the RNA metabolism of mitochondria and/or plastids. To date, the molecular function of many PPR proteins is still unknown. Here we analyzed the nucleus-encoded gene At4g19440 coding for a P-type PPR protein. Knockout of this gene interferes with normal embryo development and seed maturation. Two experimental approaches were applied to overcome lethality and to investigate the outcome of At4g19440 knockout in adult plants. These studies revealed changes in the abundance of several mitochondria-encoded transcripts. In particular, steady-state levels of dicistronic rpl5-cob RNAs were markedly reduced, whereas levels of mature ccmC and rpl2-mttB transcripts were clearly increased. Predictions according to the one repeat to one nucleotide code for PPR proteins indicate binding of the At4g19440 protein to a previously detected small RNA at the 3' termini of the dicistronic rpl5-cob transcripts. This potential interaction indicates a function of this protein in 3' end formation and stabilization of these RNA species, whereas the increase in the levels of the ccmC mRNA along with other mitochondria-encoded RNAs seems to be a secondary effect of At4g19440 knockout. Since the inactivation of At4g19440 influences the stability of several mitochondrial RNAs we call this gene MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4). This factor will be an interesting subject to study opposing effects of a single nucleus-encoded protein on mitochondrial transcript levels.
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Affiliation(s)
- Lisa Jung
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Sarah Schleicher
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Fatema Alsaied Taha
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
| | - Mizuki Takenaka
- Plant Molecular Genetics, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Stefan Binder
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069, Ulm, Germany
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12
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Fan K, Fu Q, Wei Q, Jia S, Zhao A, Wang T, Cao J, Liu Y, Ren Z, Liu Y. ZmnMAT1, a nuclear-encoded type I maturase, is required for the splicing of mitochondrial Nad1 intron 1 and Nad4 intron 2. FRONTIERS IN PLANT SCIENCE 2022; 13:1033869. [PMID: 36507372 PMCID: PMC9727264 DOI: 10.3389/fpls.2022.1033869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Maturases can specifically bind to intron-containing pre-RNAs, folding them into catalytic structures that facilitate intron splicing in vivo. Plants possess four nuclear-encoded maturase-related factors (nMAT1-nMAT4) and some maturases have been shown to involve in the splicing of different mitochondrial group II introns; however, the specific biological functions of maturases in maize are largely uncharacterized. In this study, we identified a maize ZmnMAT1 gene, which encodes a mitochondrion-localized type I maturase with an RT domain at N-terminus and an X domain at C-terminus. Loss-of-function mutation in ZmnMAT1 significantly reduced the splicing efficiencies of Nad1 intron 1 and Nad4 intron 2, and showed arrested embryogenesis and endosperm development, which may be related to impaired mitochondrial ultrastructure and function due to the destruction of the assembly and activity of complex I. Direct physical interaction was undetectable between ZmnMAT1 and the proteins associated with the splicing of Nad1 intron 1 and/or Nad4 intron 2 by yeast two-hybrid assays, suggesting the complexity of group II intron splicing in plants.
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Affiliation(s)
- Kaijian Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghui Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qianhan Wei
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sinian Jia
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Anqi Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Tengteng Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Cao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenjing Ren
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Cao SK, Liu R, Wang M, Sun F, Sayyed A, Shi H, Wang X, Tan BC. The small PPR protein SPR2 interacts with PPR-SMR1 to facilitate the splicing of introns in maize mitochondria. PLANT PHYSIOLOGY 2022; 190:1763-1776. [PMID: 35976145 PMCID: PMC9614438 DOI: 10.1093/plphys/kiac379] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 05/31/2023]
Abstract
Splicing of plant mitochondrial introns is facilitated by numerous nucleus-encoded protein factors. Although some splicing factors have been identified in plants, the mechanism underlying mitochondrial intron splicing remains largely unclear. In this study, we identified a small P-type pentatricopeptide repeat (PPR) protein containing merely four PPR repeats, small PPR protein 2 (SPR2), which is required for the splicing of more than half of the introns in maize (Zea mays) mitochondria. Null mutations of Spr2 severely impair the splicing of 15 out of the 22 mitochondrial Group II introns, resulting in substantially decreased mature transcripts, which abolished the assembly and activity of mitochondrial complex I. Consequently, embryogenesis and endosperm development were arrested in the spr2 mutants. Yeast two-hybrid, luciferase complementation imaging, bimolecular fluorescence complementation, and semi-in vivo pull-down analyses indicated that SPR2 interacts with small MutS-related domain protein PPR-SMR1, both of which are required for the splicing of 13 introns. In addition, SPR2 and/or PPR-SMR1 interact with other splicing factors, including PPR proteins EMPTY PERICARP16, PPR14, and chloroplast RNA splicing and ribosome maturation (CRM) protein Zm-mCSF1, which participate in the splicing of specific intron(s) of the 13 introns. These results prompt us to propose that SPR2/PPR-SMR1 serves as the core component of a splicing complex and possibly exerts the splicing function through a dynamic interaction with specific substrate recognizing PPR proteins in mitochondria.
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Affiliation(s)
- Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Miaodi Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hong Shi
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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14
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Sun Q, Li Y, Gong D, Hu A, Zhong W, Zhao H, Ning Q, Tan Z, Liang K, Mu L, Jackson D, Zhang Z, Yang F, Qiu F. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination. Nat Commun 2022; 13:5708. [PMID: 36175574 PMCID: PMC9522829 DOI: 10.1038/s41467-022-33513-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Maize early endosperm development is initiated in coordination with elimination of maternal nucellar tissues. However, the underlying mechanisms are largely unknown. Here, we characterize a major quantitative trait locus for maize kernel size and weight that encodes an EXPANSIN gene, ZmEXPB15. The encoded β-expansin protein is expressed specifically in nucellus, and positively controls kernel size and weight by promoting nucellus elimination. We further show that two nucellus-enriched transcription factors (TFs), ZmNAC11 and ZmNAC29, activate ZmEXPB15 expression. Accordingly, these two TFs also promote kernel size and weight through nucellus elimination regulation, and genetic analyses support their interaction with ZmEXPB15. Importantly, hybrids derived from a ZmEXPB15 overexpression line have increased kernel weight, demonstrates its potential value in breeding. Together, we reveal a pathway modulating the cellular processes of maternal nucellus elimination and early endosperm development, and an approach to improve kernel weight.
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Affiliation(s)
- Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Aoqing Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Kun Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Luyao Mu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.
- Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.
- Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
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15
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Wang Y, Yang Z, Zhang M, Ai P. A chloroplast-localized pentatricopeptide repeat protein involved in RNA editing and splicing and its effects on chloroplast development in rice. BMC PLANT BIOLOGY 2022; 22:437. [PMID: 36096762 PMCID: PMC9469629 DOI: 10.1186/s12870-022-03819-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The chloroplast is the organelle responsible for photosynthesis in higher plants. The generation of functional chloroplasts depends on the precise coordination of gene expression in the nucleus and chloroplasts and is essential for the development of plants. However, little is known about nuclear-plastid regulatory mechanisms at the early stage of chloroplast generation in rice. RESULTS In this study, we identified a rice (Oryza sativa) mutant that exhibited albino and seedling-lethal phenotypes and named it ssa1(seedling stage albino1). Transmission electron microscopy (TEM) analysis indicated that the chloroplasts of ssa1 did not have organized thylakoid lamellae and that the chloroplast structure was destroyed. Genetic analysis revealed that the albino phenotypes of ssa1 were controlled by a pair of recessive nuclear genes. Map-based cloning experiments found that SSA1 encoded a pentapeptide repeat (PPR) protein that was allelic to OSOTP51,which was previously reported to participate in Photosystem I (PSI) assembly. The albino phenotype was reversed to the wild type (WT) phenotype when the normal SSA1 sequence was expressed in ssa1 under the drive of the actin promoter. Knockout experiments further created mutants ssa1-2/1-9, which had a phenotype similar to that of ssa1. SSA1 consisted of 7 pentatricopeptide repeat domains and two C-terminal LAGLIDADG tandem sequence motifs and was located in the chloroplast. GUS staining and qRT-PCR analysis showed that SSA1 was mainly expressed in young leaves and stems. In the ssa1 mutants, plastid genes transcribed by plastid-encoded RNA polymerase decreased, while those transcribed by nuclear-encoded RNA polymerase increased at the mRNA level. Loss-of-function SSA1 destroys RNA editing of ndhB-737 and intron splicing of atpF and ycf3-2 in the plastid genome. Yeast two-hybrid and BiFC assays revealed that SSA1 physically interacted with two new RNA editing partners, OsMORF8 and OsTRXz, which have potential functions in RNA editing and chloroplast biogenesis. CONCLUSIONS Rice SSA1 encodes a pentatricopeptide repeat protein, which is targeted to the chloroplast. SSA1 regulates early chloroplast development and plays a critical role in RNA editing and intron splicing in rice. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.
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Affiliation(s)
- Yanwei Wang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Zhimin Yang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Meng Zhang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Pengfei Ai
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China.
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16
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Genome-wide transcriptome profiling of CSF virus challenged monocyte-derived macrophages provides distinct insights into immune response of Landrace and indigenous Ghurrah pigs. Genomics 2022; 114:110427. [PMID: 35803450 DOI: 10.1016/j.ygeno.2022.110427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/13/2022] [Accepted: 07/02/2022] [Indexed: 11/21/2022]
Abstract
The present study was undertaken to characterize the distinct immune response in indigenous Ghurrah and exotic Landrace pigs by challenging monocyte-derived macrophages (MDMs) with CSF virus under in-vitro conditions and assessing the variations in the transcriptome profile at 48 h post-infection (hpi). RNA-sequencing was carried out in infected and non-infected MDMs of Ghurrah (n = 3) and Landrace (n = 3) piglets prior- as well as post-stimulation. MDMs of Ghurrah showed greater immune regulation in response to CSF infection with 518 significantly differentially expressed genes (DEG) in infected versus non-infected MDMs, as compared to only 31 DEGs in Landrace MDMs. In Landrace, the principal regulators of inflammation (IL1α, IL1β and TNF) were upregulated in infected cells while in Ghurrah, these were downregulated. Overall, macrophages from indigenous Ghurrah showed more immunological dysregulation in response to virulent CSF virus infection as compared to the exotic Landrace pigs.
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17
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Sun Q, Hu A, Mu L, Zhao H, Qin Y, Gong D, Qiu F. Identification of a candidate gene underlying qHKW3, a QTL for hundred-kernel weight in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1579-1589. [PMID: 35179613 DOI: 10.1007/s00122-022-04055-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
qHKW3, a quantitative trait locus for hundred-kernel weight, harbors the proposed causal gene Zm00001d044081, encoding a homeobox-leucine zipper protein (ATHB-4) that might affect kernel size and weight. Kernel size and weight are key traits that contribute greatly to grain yield per year in maize (Zea mays). Here, we developed the chromosome segment substitution line (CSSL), H15-6-2, with smaller kernel size and lower kernel weight across environments compared to the background line Ye478. Histological analysis suggested that a slower kernel filling rate of H15-6-2 contributes to its small-kernel size and reduced hundred-kernel weight. We identified a quantitative trait locus (QTL) explaining 23% of the phenotypic variation in hundred-kernel weight. This QTL, qHKW3, was fine mapped to an interval of approximately 40.66-kb harboring the gene Zm00001d044081. The upstream sequence and its expression level of Zm00001d044081 in kernels at 6 days after pollination (DAP) showed obvious differences between the near-isogenic lines HKW3Ye478 and HKW3H15-6-2. We further confirmed the effects of the Zm00001d044081 promoter on maize kernel size and weight in an independent association mapping panel with 513 lines by candidate regional association analysis. We propose that Zm00001d044081, which encodes the homeobox-leucine zipper protein ATHB-4, is the causal gene of qHKW3, representing an attractive target for the genetic improvement of maize yield.
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Affiliation(s)
- Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Aoqing Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Luyao Mu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Yao Qin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China.
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18
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Yang T, Wang H, Guo L, Wu X, Xiao Q, Wang J, Wang Q, Ma G, Wang W, Wu Y. ABA-induced phosphorylation of basic leucine zipper 29, ABSCISIC ACID INSENSITIVE 19, and Opaque2 by SnRK2.2 enhances gene transactivation for endosperm filling in maize. THE PLANT CELL 2022; 34:1933-1956. [PMID: 35157077 PMCID: PMC9048887 DOI: 10.1093/plcell/koac044] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/03/2022] [Indexed: 05/23/2023]
Abstract
Opaque2 (O2) functions as a central regulator of the synthesis of starch and storage proteins and the O2 gene is transcriptionally regulated by a hub coordinator of seed development and grain filling, ABSCISIC ACID INSENSITIVE 19 (ZmABI19), in maize (Zea mays). Here, we identified a second hub coordinator, basic Leucine Zipper 29 (ZmbZIP29) that interacts with ZmABI19 to regulate O2 expression. Like zmabi19, zmbzip29 mutations resulted in a dramatic decrease of transcript and protein levels of O2 and thus a significant reduction of starch and storage proteins. zmbzip29 seeds developed slower and had a smaller size at maturity than those of the wild type. The zmbzip29;zmabi19 double mutant displayed more severe seed phenotypes and a greater reduction of storage reserves compared to the single mutants, whereas overexpression of the two transcription factors enhanced O2 expression, storage-reserve accumulation, and kernel weight. ZmbZIP29, ZmABI19, and O2 expression was induced by abscisic acid (ABA). With ABA treatment, ZmbZIP29 and ZmABI19 synergistically transactivated the O2 promoter. Through liquid chromatography tandem-mass spectrometry analysis, we established that the residues threonine(T) 57 in ZmABI19, T75 in ZmbZIP29, and T387 in O2 were phosphorylated, and that SnRK2.2 was responsible for the phosphorylation. The ABA-induced phosphorylation at these sites was essential for maximum transactivation of downstream target genes for endosperm filling in maize.
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Affiliation(s)
- Tao Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haonan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Liangxing Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Qiao Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guangjin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
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19
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Yang J, Cui Y, Zhang X, Yang Z, Lai J, Song W, Liang J, Li X. Maize PPR278 Functions in Mitochondrial RNA Splicing and Editing. Int J Mol Sci 2022; 23:ijms23063035. [PMID: 35328469 PMCID: PMC8949463 DOI: 10.3390/ijms23063035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are a large protein family in higher plants and play important roles during seed development. Most reported PPR proteins function in mitochondria. However, some PPR proteins localize to more than one organelle; functional characterization of these proteins remains limited in maize (Zea mays L.). Here, we cloned and analyzed the function of a P-subfamily PPR protein, PPR278. Loss-function of PPR278 led to a lower germination rate and other defects at the seedling stage, as well as smaller kernels compared to the wild type. PPR278 was expressed in all investigated tissues. Furthermore, we determined that PPR278 is involved in the splicing of two mitochondrial transcripts (nad2 intron 4 and nad5 introns 1 and 4), as well as RNA editing of C-to-U sites in 10 mitochondrial transcripts. PPR278 localized to the nucleus, implying that it may function as a transcriptional regulator during seed development. Our data indicate that PPR278 is involved in maize seed development via intron splicing and RNA editing in mitochondria and has potential regulatory roles in the nucleus.
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Affiliation(s)
- Jing Yang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yang Cui
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xiangbo Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Zhijia Yang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; (Y.C.); (X.Z.); (Z.Y.); (J.L.); (W.S.)
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jingang Liang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China
- Correspondence: (J.L.); (X.L.)
| | - Xinhai Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence: (J.L.); (X.L.)
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Ji C, Xu L, Li Y, Fu Y, Li S, Wang Q, Zeng X, Zhang Z, Zhang Z, Wang W, Wang J, Wu Y. The O2-ZmGRAS11 transcriptional regulatory network orchestrates the coordination of endosperm cell expansion and grain filling in maize. MOLECULAR PLANT 2022; 15:468-487. [PMID: 34848346 DOI: 10.1016/j.molp.2021.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/03/2021] [Accepted: 11/26/2021] [Indexed: 05/12/2023]
Abstract
Maize (Zea mays) endosperm filling is coordinated with cell expansion to enlarge the grain size, but the mechanism coupling the two processes is poorly understood. Starchy endosperm cells basically contain no visible vacuoles for cell expansion. During grain filling, efficient synthesis of storage compounds leads to reduced cytoplasm and thus lowered cell turgor pressure. Although bioactive gibberellins (GAs) are essential for cell expansion, they accumulate at a low level at this stage. In this study, we identified an endosperm-specific GRAS domain-containing protein (ZmGRAS11) that lacks the DELLA domain and promotes cell expansion in the filling endosperm. The zmgras11 loss-of-function mutants showed normal grain filling but delayed cell expansion, thereby resulting in reduced kernel size and weight. Overexpression of ZmGRAS11 led to larger endosperm cells and therefore increased kernel size and weight. Consistent with this, ZmGRAS11 positively regulates the expression of ZmEXPB12, which is essential for cell expansion, at the endosperm filling stage. Moreover, we found that Opaque2 (O2), a central transcription factor that regulates endosperm filling, could directly bind to the promoter of ZmGRAS11 and activate its expression. Taken together, these results suggest that endosperm cell expansion is coupled with endosperm filling, which is orchestrated by the O2-ZmGRAS11-centered transcriptional regulatory network. Our findings also provide potential targets for maize yield improvement by increasing the storage capacity of endosperm cells.
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Affiliation(s)
- Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China
| | - Yujie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxin Fu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuai Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China
| | - Xing Zeng
- College of Agronomy, Northeast Agricultural University, Harbin 150030, China
| | - Zhongqin Zhang
- Hebei Sub-center of the Chinese National Maize Improvement Center, College of Agronomy, Agricultural University of Hebei, Baoding, China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wenqin Wang
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai 200233, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China.
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai 200032, China.
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21
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MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23052670. [PMID: 35269810 PMCID: PMC8910670 DOI: 10.3390/ijms23052670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players in plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1, and thus respiratory complex I biogenesis, are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.
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22
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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23
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Feng Y, Ma Y, Feng F, Chen X, Qi W, Ma Z, Song R. Accumulation of 22 kDa α-zein-mediated nonzein protein in protein body of maize endosperm. THE NEW PHYTOLOGIST 2022; 233:265-281. [PMID: 34637530 DOI: 10.1111/nph.17796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Protein bodies (PBs), the major protein storage organelle in maize (Zea mays) endosperm, comprise zeins and numerous nonzein proteins (NZPs). Unlike zeins, how NZPs accumulate in PBs remains unclear. We characterized a maize miniature kernel mutant, mn*, that produces small kernels and is embryo-lethal. After cloning the Mn* locus, we determined that it encodes the mitochondrial 50S ribosomal protein L10 (mRPL10). MN* localized to mitochondria and PBs as an NZP; therefore, we renamed MN* Non-zein Protein 1 (NZP1). Like other mutations affecting mitochondrial proteins, mn* impaired mitochondrial function and morphology. To investigate its accumulation mechanism to PBs, we performed protein interaction assays between major zein proteins and NZP1, and found that NZP1 interacts with 22 kDa α-zein. Levels of NZP1 and 22 kDa α-zein in various opaque mutants were correlated. Furthermore, NZP1 accumulation in induced PBs depended on its interaction with 22 kDa α-zein. Comparative proteomic analysis of PBs between wild-type and opaque2 revealed additional NZPs. A new NZP with plastidial localization was also found to accumulate in induced PBs via interaction with 22 kDa α-zein. This study thus reveals a mechanism for accumulation of NZPs in PBs and suggests a potential application for the accumulation of foreign proteins in maize PBs.
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Affiliation(s)
- Yang Feng
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yafei Ma
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Fan Feng
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xinze Chen
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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24
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Fan K, Ren Z, Zhang X, Liu Y, Fu J, Qi C, Tatar W, Rasmusson AG, Wang G, Liu Y. The pentatricopeptide repeat protein EMP603 is required for the splicing of mitochondrial Nad1 intron 2 and seed development in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6933-6948. [PMID: 34279607 DOI: 10.1093/jxb/erab339] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Intron splicing is an essential event in post-transcriptional RNA processing in plant mitochondria, which requires the participation of diverse nuclear-encoded splicing factors. However, it is presently unclear how these proteins cooperatively take part in the splicing of specific introns. In this study, we characterized a nuclear-encoded mitochondrial P-type pentatricopeptide repeat (PPR) protein named EMP603. This protein is essential for splicing of intron 2 in the Nad1 gene and interacts with the mitochondria-localized DEAD-box RNA helicase PMH2-5140, the RAD52-like proteins ODB1-0814 and ODB1-5061, and the CRM domain-containing protein Zm-mCSF1. Further study revealed that the N-terminal region of EMP603 interacts with the DEAD-box of PMH2-5140, the CRM domain of Zm-mCSF1, and OBD1-5061, but not with OBD1-0814, whereas the PPR domain of EMP603 can interact with ODB1-0814, ODB1-5061, and PMH2-5140, but not with Zm-mCSF1. Defects in EMP603 severely disrupt the assembly and activity of mitochondrial complex I, leading to impaired mitochondrial function, and delayed seed development. The interactions revealed between EMP603 and PMH2-5140, ODB1-0814, ODB1-5061, and Zm-mCSF1 indicate a possible involvement of a dynamic 'spliceosome-like' complex in intron splicing, and may accelerate the elucidation of the intron splicing mechanism in plant mitochondria.
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Affiliation(s)
- Kaijian Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenjing Ren
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunlai Qi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wurinile Tatar
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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25
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Li X, Sun M, Liu S, Teng Q, Li S, Jiang Y. Functions of PPR Proteins in Plant Growth and Development. Int J Mol Sci 2021; 22:11274. [PMID: 34681932 PMCID: PMC8537650 DOI: 10.3390/ijms222011274] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.
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Affiliation(s)
- Xiulan Li
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (M.S.); (S.L.); (Q.T.); (S.L.)
| | | | | | | | | | - Yueshui Jiang
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (M.S.); (S.L.); (Q.T.); (S.L.)
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26
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Liu X, Zhang X, Cao R, Jiao G, Hu S, Shao G, Sheng Z, Xie L, Tang S, Wei X, Hu P. CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1724-1739. [PMID: 34219386 DOI: 10.1111/jipb.13147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/30/2021] [Indexed: 05/24/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play important roles in the post-transcriptional modification of organellar RNAs in plants. However, the function of most PPR proteins remains unknown. Here, we characterized the rice (Oryza sativa L.) chlorophyll deficient 4 (cde4) mutant which exhibits an albino phenotype during early leaf development, with decreased chlorophyll contents and abnormal chloroplasts at low-temperature (20°C). Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts. In the cde4 mutant, plastid-encoded polymerase (PEP)-dependent transcript levels were significantly reduced, but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20°C. CDE4 directly binds to the transcripts of the chloroplast genes rpl2, ndhA, and ndhB. Intron splicing of these transcripts was defective in the cde4 mutant at 20°C, but was normal at 32°C. Moreover, CDE4 interacts with the guanylate kinase VIRESCENT 2 (V2); overexpression of V2 enhanced CDE4 protein stability, thereby rescuing the cde4 phenotype at 20°C. Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under low-temperature conditions.
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Affiliation(s)
- Xinyong Liu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xichun Zhang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
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Zhang D, Chen C, Wang H, Niu E, Zhao P, Fang S, Zhu G, Shang X, Guo W. Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA. Genetics 2021; 217:1-17. [PMID: 33683356 DOI: 10.1093/genetics/iyaa017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2020] [Indexed: 12/27/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins encoded by nuclear genomes can bind to organellar RNA and are involved in the regulation of RNA metabolism. However, the functions of many PPR proteins remain unknown in plants, especially in polyploidy crops. Here, through a map-based cloning strategy and Clustered regularly interspaced short palindromic repeats/cas9 (CRISPR/cas9) gene editing technology, we cloned and verified an allotetraploid cotton immature fiber (im) mutant gene (GhImA) encoding a PPR protein in chromosome A03, that is associated with the non-fluffy fiber phenotype. GhImA protein targeted mitochondrion and could bind to mitochondrial nad7 mRNA, which encodes the NAD7 subunit of Complex I. GhImA and its homolog GhImD had the same function and were dosage-dependent. GhImA in the im mutant was a null allele with a 22 bp deletion in the coding region. Null GhImA resulted in the insufficient GhIm dosage, affected mitochondrial nad7 pre-mRNA splicing, produced less mature nad7 transcripts, and eventually reduced Complex I activities, up-regulated alternative oxidase metabolism, caused reactive oxygen species (ROS) burst and activation of stress or hormone response processes. This study indicates that the GhIm protein participates in mitochondrial nad7 splicing, affects respiratory metabolism, and further regulates cotton fiber development via ATP supply and ROS balance.
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Affiliation(s)
- Dayong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Erli Niu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyue Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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Mukhopadhyay J, Hausner G. Organellar Introns in Fungi, Algae, and Plants. Cells 2021; 10:cells10082001. [PMID: 34440770 PMCID: PMC8393795 DOI: 10.3390/cells10082001] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022] Open
Abstract
Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.
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MESH Headings
- Evolution, Molecular
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Plant
- Genome, Fungal
- Genome, Plant
- Introns
- Organelles/genetics
- Organelles/metabolism
- RNA Splicing
- RNA Stability
- RNA, Algal/genetics
- RNA, Algal/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Transcription, Genetic
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Xu R, Li Y, Sui Z, Lan T, Song W, Zhang M, Zhang Y, Xing J. A C-terminal encoded peptide, ZmCEP1, is essential for kernel development in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5390-5406. [PMID: 34104938 DOI: 10.1093/jxb/erab224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
C-terminal encoded peptides (CEPs) are peptide hormones which act as mobile signals coordinating important developmental programs. Previous studies have unraveled that CEPs are able to regulate plant growth and abiotic stress via cell-to-cell communication in Arabidopsis and rice; however, little is known about their roles in maize. Here, we examined the spatiotemporal expression pattern of ZmCEP1 and showed that ZmCEP1 is highly expressed in young ears and tassels of maize, particularly in the vascular bundles of ears. Heterologous expression of ZmCEP1 in Arabidopsis results in smaller plants and seed size. Similarly, overexpression of ZmCEP1 in maize decreased the plant and ear height, ear length, kernel size, and 100-kernel weight. Consistently, exogenous application of the synthesized ZmCEP1 peptide to the roots of Arabidopsis and maize inhibited root elongation. Knock-out of ZmCEP1 through CRISPR/Cas9 significantly increased plant and ear height, kernel size and 100-kernel weight. Transcriptome analysis revealed that knock-out of ZmCEP1 up-regulated a subset of genes involved in nitrogen metabolism, nitrate transport, sugar transport and auxin response. Thus, these results provide new insights into the genetic and molecular function of ZmCEP1 in regulating kernel development and plant growth, providing novel opportunities for maize breeding.
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Affiliation(s)
- Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yufeng Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Tianyu Lan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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30
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Yu M, Wu M, Ren Y, Wang Y, Li J, Lei C, Sun Y, Bao X, Wu H, Yang H, Pan T, Wang Y, Jing R, Yan M, Zhang H, Zhao L, Zhao Z, Zhang X, Guo X, Cheng Z, Yang B, Jiang L, Wan J. Rice FLOURY ENDOSPERM 18 encodes a pentatricopeptide repeat protein required for 5' processing of mitochondrial nad5 messenger RNA and endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:834-847. [PMID: 33283410 DOI: 10.1111/jipb.13049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins, composing one of the largest protein families in plants, are involved in RNA binding and regulation of organelle RNA metabolism at the post-transcriptional level. Although several PPR proteins have been implicated in endosperm development in rice (Oryza sativa), the molecular functions of many PPRs remain obscure. Here, we identified a rice endosperm mutant named floury endosperm 18 (flo18) with pleiotropic defects in both reproductive and vegetative development. Map-based cloning and complementation tests showed that FLO18 encodes a mitochondrion-targeted P-type PPR protein with 15 PPR motifs. Mitochondrial function was disrupted in the flo18 mutant, as evidenced by decreased assembly of Complex I in the mitochondrial electron transport chain and altered mitochondrial morphology. Loss of FLO18 function resulted in defective 5'-end processing of mitochondrial nad5 transcripts encoding subunit 5 of nicotinamide adenine dinucleotide hydrogenase. These results suggested that FLO18 is involved in 5'-end processing of nad5 messenger RNA and plays an important role in mitochondrial function and endosperm development.
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Affiliation(s)
- Mingzhou Yu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingming Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingfang Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yinglun Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuhao Bao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongming Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hang Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tian Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongfei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruonan Jing
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengyuan Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Houda Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bing Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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31
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Gong D, Tan Z, Zhao H, Pan Z, Sun Q, Qiu F. Fine mapping of a kernel length-related gene with potential value for maize breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1033-1045. [PMID: 33459823 DOI: 10.1007/s00122-020-03749-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
A key candidate gene for maize kernel length was fine mapped to an interval of 942 kb; the locus significantly increases kernel length (KL) and hundred-kernel weight (HKW). Kernel size is a major determinant of yield in cereals. Kernel length, one of the determining factors of kernel size, is a target trait for both domestication and artificial breeding. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for kernel length in maize. In this project, a novel major QTL, named qKL9, controlling maize kernel length was identified. We verified the authenticity and stability of qKL9 via BC2F2 and BC3F1 populations, respectively, and ultimately mapped qKL9 to an ~ 942-kb genomic interval by testing the progenies of recombination events derived from BC3F2 and BC4F2 populations in multiple environments. Additionally, one new line (McqKL9-A) containing the ~ 942-kb segment was screened from the BC4F2 population. Combining transcriptome analysis between McqKL9-A and Mc at 6, 9 and 14 days after pollination and candidate regional association mapping, Zm00001d046723 was preliminarily identified as the key candidate gene for qKL9. Importantly, the replacement in the Mc line of the Mc's alleles by the V671's alleles in the qKL9 region improved the performances of single-cross hybrids obtained with elite lines, illustrating the potential value of this QTL for the genetic improvement in maize kernel-related traits. These findings facilitate molecular breeding for kernel size and cloning of the gene underlying qKL9, shedding light on the genetic basis of kernel size in maize.
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Affiliation(s)
- Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China.
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32
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Wang L, Zhang W, Liu S, Tian Y, Liu X, Yan H, Cai Y, Teng X, Dong H, Chen R, Jiang X, Wang Y, Wan J. Rice FLOURY SHRUNKEN ENDOSPERM 5 Encodes a Putative Plant Organelle RNA Recognition Protein that Is Required for cis-Splicing of Mitochondrial nad4 Intron 1. RICE (NEW YORK, N.Y.) 2021; 14:29. [PMID: 33689034 PMCID: PMC7947098 DOI: 10.1186/s12284-021-00463-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The sequences of several important mitochondrion-encoded genes involved in respiration in higher plants are interrupted by introns. Many nuclear-encoded factors are involved in splicing these introns, but the mechanisms underlying this splicing remain unknown. RESULTS We isolated and characterized a rice mutant named floury shrunken endosperm 5 (fse5). In addition to having floury shrunken endosperm, the fse5 seeds either failed to germinate or produced seedlings which grew slowly and died ultimately. Fse5 encodes a putative plant organelle RNA recognition (PORR) protein targeted to mitochondria. Mutation of Fse5 hindered the splicing of the first intron of nad4, which encodes an essential subunit of mitochondrial NADH dehydrogenase complex I. The assembly and NADH dehydrogenase activity of complex I were subsequently disrupted by this mutation, and the structure of the mitochondria was abnormal in the fse5 mutant. The FSE5 protein was shown to interact with mitochondrial intron splicing factor 68 (MISF68), which is also a splicing factor for nad4 intron 1 identified previously via yeast two-hybrid (Y2H) assays. CONCLUSION Fse5 which encodes a PORR domain-containing protein, is essential for the splicing of nad4 intron 1, and loss of Fse5 function affects seed development and seedling growth.
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Affiliation(s)
- Liang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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33
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Zheng P, Liu Y, Liu X, Huang Y, Sun F, Wang W, Chen H, Jan M, Zhang C, Yuan Y, Tan BC, Du H, Tu J. OsPPR939, a nad5 splicing factor, is essential for plant growth and pollen development in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:923-940. [PMID: 33386861 PMCID: PMC7925476 DOI: 10.1007/s00122-020-03742-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/25/2020] [Indexed: 05/18/2023]
Abstract
P-subfamily PPR protein OsPPR939, which can be phosphorylated by OsS6K1, regulates plant growth and pollen development by involving in the splicing of mitochondrial nad5 introns 1, 2, and 3. In land plants, pentatricopeptide repeat (PPR) proteins play key roles in mitochondrial group II intron splicing, but how these nucleus-encoded proteins are imported into mitochondria is unknown. To date, a few PPR proteins have been characterized in rice (Oryza sativa). Here, we demonstrate that the mitochondrion-localized P-subfamily PPR protein OsPPR939 is required for the splicing of nad5 introns 1, 2, and 3 in rice. Complete knockout or partial disruption of OsPPR939 function resulted in different degrees of growth retardation and pollen sterility. The dramatically reduced splicing efficiency of these introns in osppr939-4 and osppr939-5 led to reduced mitochondrial complex I abundance and activity and enhanced expression of alternative respiratory pathway genes. Complementation with OsPPR939 rescued the defective plant morphology of osppr939-4 and restored its decreased splicing efficiency of nad5 introns 1, 2, and 3. Therefore, OsPPR939 plays crucial roles in plant growth and pollen development by splicing mitochondrial nad5 introns 1, 2, and 3. More importantly, the 12th amino acid Ser in the N-terminal targeting sequence of OsPPR939 is phosphorylated by OsS6K1, and truncated OsPPR939 with a non-phosphorylatable S12A mutation in its presequence could not be imported into mitochondria, suggesting that phosphorylation of this amino acid plays an important role in the mitochondrial import of OsPPR939. To our knowledge, the 12th residue Ser on OsPPR939 is the first experimentally proven phosphorylation site in PPR proteins. Our results provide a basis for investigating the regulatory mechanism of PPR proteins at the post-translational level.
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Affiliation(s)
- Peng Zheng
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujun Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yuqing Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wenyi Wang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Mehmood Jan
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Cuicui Zhang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yue Yuan
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hao Du
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| | - Jumin Tu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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34
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Chen W, Cui Y, Wang Z, Chen R, He C, Liu Y, Du X, Liu Y, Fu J, Wang G, Wang J, Gu R. Nuclear-Encoded Maturase Protein 3 Is Required for the Splicing of Various Group II Introns in Mitochondria during Maize (Zea mays L.) Seed Development. ACTA ACUST UNITED AC 2021; 62:293-305. [DOI: 10.1093/pcp/pcaa161] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/05/2020] [Indexed: 11/12/2022]
Abstract
Abstract
Splicing of plant organellar group II introns from precursor-RNA transcripts requires the assistance of nuclear-encoded splicing factors. Maturase (nMAT) is one such factor, as its three homologs (nMAT1, 2 and 4) have been identified as being required for the splicing of various mitochondrial introns in Arabidopsis. However, the function of nMAT in maize (Zea mays L.) is unknown. In this study, we identified a seed development mutant, empty pericarp 2441 (emp2441) from maize, which showed severely arrested embryogenesis and endosperm development. Positional cloning and transgenic complementation assays revealed that Emp2441 encodes a maturase-related protein, ZmnMAT3. ZmnMAT3 is highly expressed during seed development and its protein locates to the mitochondria. The loss of function of ZmnMAT3 resulted in the reduced splicing efficiency of various mitochondrial group II introns, particularly of the trans-splicing of nad1 introns 1, 3 and 4, which consequently abolished the transcript of nad1 and severely impaired the assembly and activity of mitochondrial complex I. Moreover, the Zmnmat3 mutant showed defective mitochondrial structure and exhibited expression and activity of alternative oxidases. These results indicate that ZmnMAT3 is essential for mitochondrial complex I assembly during kernel development in maize.
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Affiliation(s)
- Weiwei Chen
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zheyuan Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Rongrong Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuemei Du
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Cao SK, Liu R, Sayyed A, Sun F, Song R, Wang X, Xiu Z, Li X, Tan BC. Regulator of Chromosome Condensation 1-Domain Protein DEK47 Functions on the Intron Splicing of Mitochondrial Nad2 and Seed Development in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:695249. [PMID: 34408760 PMCID: PMC8365749 DOI: 10.3389/fpls.2021.695249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 05/10/2023]
Abstract
In flowering plants, mitochondrial genes contain approximately 20-26 introns. Splicing of these introns is essential for mitochondrial gene expression and function. Recent studies have revealed that both nucleus- and mitochondrion-encoded factors are required for intron splicing, but the mechanism of splicing remains largely unknown. Elucidation of the mechanism necessitates a complete understanding of the splicing factors. Here, we report the identification of a regulator of chromosome condensation 1 (RCC1)-domain protein DEK47 that is required for mitochondrial intron splicing and seed development in maize. Loss of function in Dek47 severely arrests embryo and endosperm development, resulting in a defective kernel (dek) phenotype. DEK47 harbors seven RCC1 domains and is targeted to mitochondria. Null mutation of DEK47 causes a deficiency in the splicing of all four nad2 introns, abolishing the production of mature nad2 transcript and resulting in the disassembly and severely reduced activity of mitochondrial complex I. In response, the expression of the alternative oxidase AOX2 is sharply increased in dek47. These results indicate that Dek47 is required for the splicing of all the nad2 introns in mitochondria, and essential for complex I assembly, and kernel development in maize.
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Affiliation(s)
- Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Ruolin Song
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihui Xiu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaojie Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Bao-Cai Tan,
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Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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Fan K, Peng Y, Ren Z, Li D, Zhen S, Hey S, Cui Y, Fu J, Gu R, Wang J, Wang G, Li L. Maize Defective Kernel605 Encodes a Canonical DYW-Type PPR Protein that Edits a Conserved Site of nad1 and Is Essential for Seed Nutritional Quality. PLANT & CELL PHYSIOLOGY 2020; 61:1954-1966. [PMID: 32818255 DOI: 10.1093/pcp/pcaa110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins involved in mitochondrial RNA cytidine (C)-to-uridine (U) editing mostly result in stagnant embryo and endosperm development upon loss of function. However, less is known about PPRs that are involved in farinaceous endosperm formation and maize quality. Here, we cloned a maize DYW-type PPR Defective Kernel605 (Dek605). Mutation of Dek605 delayed seed and seedling development. Mitochondrial transcript analysis of dek605 revealed that loss of DEK605 impaired C-to-U editing at the nad1-608 site and fails to alter Ser203 to Phe203 in NAD1 (dehydrogenase complex I), disrupting complex I assembly and reducing NADH dehydrogenase activity. Meanwhile, complexes III and IV in the cytochrome pathway, as well as AOX2 in the alternative respiratory pathway, are dramatically increased. Interestingly, the dek605 mutation resulted in opaque endosperm and increased levels of the free amino acids alanine, aspartic acid and phenylalanine. The down- and upregulated genes mainly involved in stress response-related and seed dormancy-related pathways, respectively, were observed after transcriptome analysis of dek605 at 12 d after pollination. Collectively, these results indicate that Dek605 specifically affects the single nad1-608 site and is required for normal seed development and resulted in nutritional quality relevant amino acid accumulation.
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Affiliation(s)
- Kaijian Fan
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yixuan Peng
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Zhenjing Ren
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Delin Li
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Sihan Zhen
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Stefan Hey
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Yu Cui
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Jianhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Guoying Wang
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
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Ren RC, Yan XW, Zhao YJ, Wei YM, Lu X, Zang J, Wu JW, Zheng GM, Ding XH, Zhang XS, Zhao XY. The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize. BMC PLANT BIOLOGY 2020; 20:553. [PMID: 33297963 PMCID: PMC7727260 DOI: 10.1186/s12870-020-02765-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/01/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. RESULTS In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291). CONCLUSIONS Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.
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Affiliation(s)
- Ru Chang Ren
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xu Wei Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, PR China
| | - Jie Zang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xin Hua Ding
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China.
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Dai D, Jin L, Huo Z, Yan S, Ma Z, Qi W, Song R. Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6246-6261. [PMID: 32710615 DOI: 10.1093/jxb/eraa348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/21/2020] [Indexed: 05/21/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.
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Affiliation(s)
- Dawei Dai
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Lifang Jin
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenzhen Huo
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shumei Yan
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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40
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Yang W, Zheng L, He Y, Zhu L, Chen X, Tao Y. Fine mapping and candidate gene prediction of a major quantitative trait locus for tassel branch number in maize. Gene 2020; 757:144928. [PMID: 32622989 DOI: 10.1016/j.gene.2020.144928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/16/2020] [Accepted: 06/27/2020] [Indexed: 11/16/2022]
Abstract
Tassel branch number (TBN) is the principal component of tassel inflorescence architecture in the maize plant. TBN is believed to be controlled by a set of quantitative trait loci (QTLs). However, it is necessary to identify and genetically evaluate these QTLs before the TBN can be improved upon using a molecular breeding approach. Therefore, in this study, we developed the chromosome segment introgression line (CSIL) TBN1 with the Zong31 (Z31) background and a higher TBN, and then we utilized the CSIL-TBN1-derived populations and identified a major QTL, qTBN6a, by linkage analysis. Fine mapping of the qTBN6a QTL was validated using a set of sub-CSILs and located in a 240-kb genomic region (Bin6.07) in B73RefGen_v4. One allele included in the introgression fragment had a positive effect, noticeably increasing the TBN and demonstrating the potential to improve the TBN of Z31. Afterward, in the qTBN6a interval, gene expression, sequence alignment, functional analysis, and the analysis of motifs in the 5' UTR suggested that candidate genes of qTBN6a are important functional genes at the early stage of immature infected tassel development. Among these candidate genes, a long W22::Mu-insertion/deletion in exon one and an 11-bp insertion/deletion in the promoter region may affect the variation of the qTBN6a QTL observed between Z31 and TBN1. In addition, the candidate genes of qTBN6a were found to encode a pentatricopeptide repeat (PPR)-containing protein and a histone deacetylase (HDA), which are known to be closely associated with RNA editing and stability and chromatin state activity for the transcription of gene expression, respectively. Finally, a model of qTBN6a based on the synergistic regulation of PPR and HDA for the maintenance of inflorescence meristem (IM) identity and its differentiation to the branch meristem (BM) in TBN1 was suggested. Collectively, our results provide an available locus for the molecular improvement of TBN and the isolation of functional genes underlying this QTL.
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Affiliation(s)
- Weifeng Yang
- Hebei Sub-center of Chinese National Maize Improvement Center, North China Key Laboratory for Crop Germplasm Resource of Education Ministry, College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, PR China
| | - Lizhen Zheng
- Hebei Sub-center of Chinese National Maize Improvement Center, North China Key Laboratory for Crop Germplasm Resource of Education Ministry, College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, PR China
| | - Yuan He
- Hebei Sub-center of Chinese National Maize Improvement Center, North China Key Laboratory for Crop Germplasm Resource of Education Ministry, College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, PR China
| | - Liying Zhu
- Hebei Sub-center of Chinese National Maize Improvement Center, North China Key Laboratory for Crop Germplasm Resource of Education Ministry, College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, PR China
| | - Xuqing Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, PR China.
| | - Yongsheng Tao
- Hebei Sub-center of Chinese National Maize Improvement Center, North China Key Laboratory for Crop Germplasm Resource of Education Ministry, College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, PR China.
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Ichinose M, Ishimaru A, Sugita C, Nakajima K, Kawaguchi Y, Sugita M. Two Novel PLS-Class Pentatricopeptide Repeat Proteins Are Involved in the Group II Intron Splicing of Mitochondrial Transcripts in the Moss Physcomitrella patens. PLANT & CELL PHYSIOLOGY 2020; 61:1687-1698. [PMID: 32525534 DOI: 10.1093/pcp/pcaa070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5' region of nad5 exon 4 and the bulged A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that a certain set of PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.
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Affiliation(s)
- Mizuho Ichinose
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601 Japan
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Airi Ishimaru
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | - Chieko Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | - Kensaku Nakajima
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | | | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
- Graduate School of Information Science, Nagoya University, Nagoya, 464-8601 Japan
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42
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Lu C, Xie Z, Yu F, Tian L, Hao X, Wang X, Chen L, Li D. Mitochondrial ribosomal protein S9M is involved in male gametogenesis and seed development in Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:655-667. [PMID: 32141186 DOI: 10.1111/plb.13108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Mitochondrial function is critical for cell vitality in all eukaryotes including plants. Although plant mitochondria contain many proteins, few have been studied in the context of plant development and physiology. We used knock-down mutant RPS9M to study its important role in male gametogenesis and seed development in Arabidopsis thaliana. Knock-down of RPS9M in the rps9m-3 mutant led to abnormal pollen development and impaired pollen tube growth. In addition, both embryo and endosperm development were affected. Phenotype analysis revealed that the rps9m-3 mutant contained a lower amount of endosperm and nuclear proteins, and both embryo cell division and embryo pattern were affected, resulting in an abnormal and defective embryo. Lowering the level of RPS9M in rps9m-3 affects mitochondrial ribosome biogenesis, energy metabolism and production of ROS. Our data revealed that RPS9M plays important roles in normal gametophyte development and seed formation, possibly by sustaining mitochondrial function.
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Affiliation(s)
- C Lu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Z Xie
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - F Yu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - L Tian
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - X Hao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - X Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - L Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - D Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
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43
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Liu R, Cao SK, Sayyed A, Xu C, Sun F, Wang X, Tan BC. The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize. Int J Mol Sci 2020; 21:ijms21114047. [PMID: 32516991 PMCID: PMC7312232 DOI: 10.3390/ijms21114047] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate. These results demonstrate that PPR18 is required for the cis-splicing of nad4 intron 1 in mitochondria, and critical to complex I assembly and seed development in maize.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
- Correspondence:
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Wang HC, Sayyed A, Liu XY, Yang YZ, Sun F, Wang Y, Wang M, Tan BC. SMALL KERNEL4 is required for mitochondrial cox1 transcript editing and seed development in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:777-792. [PMID: 31332949 DOI: 10.1111/jipb.12856] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
In land plants, cytidine-to-uridine (C-to-U) editing of organellar transcripts is an important post-transcriptional process, which is considered to remediate DNA genetic mutations to restore the coding of functional proteins. Pentatricopeptide repeat (PPR) proteins have key roles in C-to-U editing. Owing to its large number, however, the biological functions of many PPR proteins remain to be identified. Through characterizing a small kernel4 (smk4) mutant, here we report the function of Smk4 and its role in maize growth and development. Null mutation of Smk4 slows plant growth and development, causing small plants, delayed flowering time, and small kernels. Cloning revealed that Smk4 encodes a new E-subclass PPR protein, and localization indicated that SMK4 is exclusively localized in mitochondria. Loss of Smk4 function abolishes C-to-U editing at position 1489 of the cytochrome c oxidase1 (cox1) transcript, causing an amino acid change from serine to proline at 497 in Cox1. Cox1 is a core component of mitochondrial complex IV. Indeed, complex IV activity is reduced in the smk4, along with drastically elevated expression of alternative oxidases (AOX). These results indicate that SMK4 functions in the C-to-U editing of cox1-1489, and this editing is crucial for mitochondrial complex IV activity, plant growth, and kernel development in maize.
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Affiliation(s)
- Hong-Chun Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xin-Yuan Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yan-Zhuo Yang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yong Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Miaodi Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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Marchetti F, Cainzos M, Shevtsov S, Córdoba JP, Sultan LD, Brennicke A, Takenaka M, Pagnussat G, Ostersetzer-Biran O, Zabaleta E. Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2020; 61:1080-1094. [PMID: 32163154 PMCID: PMC7295397 DOI: 10.1093/pcp/pcaa028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/08/2020] [Indexed: 05/14/2023]
Abstract
The Arabidopsis genome encodes >450 proteins containing the pentatricopeptide repeat (PPR) motif. The PPR proteins are classified into two groups, termed as P and P Long-Short (PLS) classes. Typically, the PLS subclass proteins are mainly involved in the RNA editing of mitochondrial and chloroplast transcripts, whereas most of the analyzed P subclass proteins have been mainly implicated in RNA metabolism, such as 5' or 3' transcript stabilization and processing, splicing and translation. Mutations of PPR genes often result in embryogenesis and altered seedling developmental defect phenotypes, but only a limited number of ppr mutants have been characterized in detail. In this report, we show that null mutations in the EMB2794 gene result in embryo arrest, due to altered splicing of nad2 transcripts in the Arabidopsis mitochondria. In angiosperms, nad2 has five exons that are transcribed individually from two mitochondrial DNA regions. Biochemical and in vivo analyses further indicate that recombinant or transgenic EMB2794 proteins bind to the nad2 pre-mRNAs in vitro as well as in vivo, suggesting a role for this protein in trans-splicing of nad2 intron 2 and possibly in the stability of the second pre-mRNA of nad2. Homozygous emb2794 lines, showing embryo-defective phenotypes, can be partially rescued by the addition of sucrose to the growth medium. Mitochondria of rescued homozygous mutant plants contain only traces of respiratory complex I, which lack the NADH-dehydrogenase activity.
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Affiliation(s)
- Fernanda Marchetti
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Maximiliano Cainzos
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Sofía Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Juan Pablo Córdoba
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Laure Dora Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Axel Brennicke
- Institut für, Molekulare Botanik, Universität Ulm, Ulm 89069, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Gabriela Pagnussat
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 919040 Jerusalem, Israel
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas (IIB)-Universidad Nacional de Mar del Plata (UNMdP)-CONICET, Funes 3250 3er nivel, 7600 Mar del Plata, Argentina
- Corresponding author: E-mail, ; Fax, +54 223 475 30 30
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Ren RC, Wang LL, Zhang L, Zhao YJ, Wu JW, Wei YM, Zhang XS, Zhao XY. DEK43 is a P-type pentatricopeptide repeat (PPR) protein responsible for the Cis-splicing of nad4 in maize mitochondria. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:299-313. [PMID: 31119902 DOI: 10.1111/jipb.12843] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/20/2019] [Indexed: 05/23/2023]
Abstract
Mitochondria, the main energy transducers in plant cells, require the proper assembly of respiratory chain complexes I-V for their function. The NADH dehydrogenase 4 (nad4) gene encodes mitochondrial respiratory chain complex I subunit IV, but the mechanism underlying nad4 transcript splicing is unclear. Here, we report that the P-type pentatricopeptide repeat (PPR) protein DEFECTIVE KERNEL 43 (DEK43) is responsible for cis-splicing of the nad4 transcript in maize. We demonstrate that DEK43 localizes to both the nucleus and mitochondria. The mutation of Dek43 resulted in embryo-lethal and light-colored defective kernels. Among the 22 mitochondrial group II introns, the splicing efficiency of nad4 introns 1 and 3 was reduced by up to 50% compared to the wild type. The levels of complex I and supercomplex I+III2 were also reduced in dek43. Furthermore, in-gel NADH dehydrogenase assays indicated that the activities of these complexes were significantly reduced in dek43. Further, the mitochondrial ultrastructure was altered in the mutant. Together, our findings indicate that DEK43, a dual-localized PPR protein, plays an important role in maintaining mitochondrial function and maize kernel development.
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Affiliation(s)
- Ru Chang Ren
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Li Li Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Lin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
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Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development. Sci Rep 2020; 10:2008. [PMID: 32029763 PMCID: PMC7005036 DOI: 10.1038/s41598-020-58495-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022] Open
Abstract
As one of the best-studied RNA binding proteins in plant, pentatricopeptide repeats (PPRs) protein are mainly targeted to mitochondria and/or chloroplasts for RNA processing to regulate the biogenesis and function of the organelles, but its molecular mechanism and role in development remain to be further revealed. Here, we identified a mitochondria-localized P-type small PPR protein, MITOCHONDRION-MEDIATED GROWTH DEFECT 1 (MID1) that is crucial for Arabidopsis development. Mutation in MID1 causes retarded embryo development and stunted plant growth with defects in cell expansion and proliferation. Molecular experiments showed that MID1 is required for the splicing of the nad2 intron 1 in mitochondria. Consistently, mid1 plants display significant reduction in the abundance and activity of mitochondrial respiration complex I, accompanied by abnormal mitochondrial morphology and energy metabolism. Furthermore, MID1 is associated with other trans-factors involved in NICOTINAMIDE ADENINE DINUCLEOTIDE HYDROGEN (NADH) DEHYDROGENASE SUBUNIT 2 (nad2) intron 1 splicing, and interacts directly with itself and MITOCHONDRIAL STABILITY FACTOR 1 (MTSF1). This suggests that MID1 most likely functions as a dimer for nad2 intron 1 splicing. Together, we characterized a novel PPR protein MID1 for nad2 intron 1 splicing.
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Wu MW, Zhao H, Zhang JD, Guo L, Liu CM. RADICLELESS 1 (RL1)-mediated nad4 intron 1 splicing is crucial for embryo and endosperm development in rice (Oryza sativa L.). Biochem Biophys Res Commun 2020; 523:220-225. [DOI: 10.1016/j.bbrc.2019.11.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/27/2022]
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Yang YZ, Ding S, Wang Y, Wang HC, Liu XY, Sun F, Xu C, Liu B, Tan BC. PPR20 Is Required for the cis-Splicing of Mitochondrial nad2 Intron 3 and Seed Development in Maize. PLANT & CELL PHYSIOLOGY 2020; 61:370-380. [PMID: 31670803 DOI: 10.1093/pcp/pcz204] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/22/2019] [Indexed: 05/02/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are helical repeat RNA-binding proteins that function in RNA processing by conferring sequence-specific RNA-binding activity. Owing to the lethality of PPR mutants, functions of many PPR proteins remain obscure. In this study, we report the function of PPR20 in intron splicing in mitochondria and its role in maize seed development. PPR20 is a P-type PPR protein targeted to mitochondria. The ppr20 mutants display slow embryo and endosperm development. Null mutation of PPR20 severely reduces the cis-splicing of mitochondrial nad2 intron 3, resulting in reduction in the assembly and activity of mitochondrial complex I. The ppr20-35 allele with a Mu insertion in the N-terminal region shows a much weaker phenotype. Molecular analyses revealed that the mutant produces a truncated transcript, coding for PPR20ΔN120 lacking the N-terminal 120 amino acids. Subcellular localization revealed that PPR20ΔN120:GFP is able to target to mitochondria as well, suggesting the sequence diversity of the mitochondrial targeting peptides. Another mutant zm_mterf15 was also found to be impaired in the splicing of mitochondrial nad2 intron 3. Further analyses are required to identify the exact function of PPR20 and Zm_mTERF15 in the splicing of nad2 intron 3.
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Affiliation(s)
- Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Shuo Ding
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hong-Chun Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Chunhui Xu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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50
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Liu M, Tan X, Yang Y, Liu P, Zhang X, Zhang Y, Wang L, Hu Y, Ma L, Li Z, Zhang Y, Zou C, Lin H, Gao S, Lee M, Lübberstedt T, Pan G, Shen Y. Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:207-221. [PMID: 31199064 PMCID: PMC6920160 DOI: 10.1111/pbi.13188] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/26/2019] [Accepted: 06/01/2019] [Indexed: 05/14/2023]
Abstract
Kernel size-related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10-6 ) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10-3 ) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable-effect SNPs and the co-localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co-localized SNPs, of which zma-miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma-miR164e resulted in the down-regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker-assisted selection (MAS) for high-yield breeding in maize.
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Affiliation(s)
- Min Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaolong Tan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yan Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Peng Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaoxiang Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yinchao Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yu Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Michael Lee
- Department of AgronomyIowa State UniversityAmesIAUSA
| | | | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (In preparation)ChengduChina
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