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Journal of Integrative Plant Biology 2021年第4期63卷 613-627页

作者： Dawei Dai Zeyang Ma rentao song State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterBeijing Key Laboratory of Crop Genetic ImprovementJoint International Research Laboratory of Crop Molecular BreedingCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Shanghai Key Laboratory of Bio-Energy Crops Plant Science CenterSchool of Life SciencesShanghai UniversityShanghai 200444China

Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental *** high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed *** spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments:the basal endosperm transfer layer(BETL),aleurone layer(AL),starchy endosperm(SE),and embryo-surrounding region(ESR).Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary,there have been some exciting advances,such as the identification of OPAQUE11(O11)as a central hub of the maize endosperm regulatory network connecting endosperm development,nutrient metabolism,and stress responses,and the discovery that the endosperm adjacent to scutellum(EAS)serves as a dynamic interface for endosperm-embryo *** addition,several genes that function in BETL development,AL differentiation,and the endosperm cell cycle have been identified,such as ZmSWEET4c,Thk1,and Dek15,***,we focus on current advances in understanding the molecular factors involved in BETL,AL,SE,ESR,and EAS development,including the specific transcriptional regulatory networks that function in each compartment during endosperm development.

关键词： endosperm development maize transcriptional regulatory network

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Dek42 encodes an RNA-binding protein that affects alternative pre-m RNA splicing and maize kernel development

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Journal of Integrative Plant Biology 2019年第6期61卷 728-748页

作者： Yi Zuo Fan Feng Weiwei Qi rentao song State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterBeijing Key Laboratory of Crop Genetic ImprovementJoint International Research Laboratory of Crop Molecular BreedingCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Shanghai Key Laboratory of Bio-Energy Crops Plant Science CenterSchool of Life SciencesShanghai UniversityShanghai 200444China

RNA-binding proteins (RBPs) play an important role in post-transcriptional gene regulation. However, the functions of RBPs in plants remain poorly understood. Maize kernel mutant dek42 has small defective kernels and lethal seedlings. Dek42 was cloned by Mutator tag isolation and further confirmed by an independent mutant allele and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 materials. Dek42 encodes an RRM_RBM48 type RNA-binding protein that localizes to the nucleus. Dek42 is constitutively expressed in various maize tissues. The dek42 mutation caused a significant reduction in the accumulation of DEK42 protein in mutant kernels. RNA-seq analysis showed that the dek42 mutation significantly disturbed the expression of thousands of genes during maize kernel development. Sequence analysis also showed that the dek42 mutation significantly changed alternative splicing in expressed genes, which were especially enriched for the U12-type intron-retained type. Yeast two-hybrid screening identified SF3a1 as a DEK42-interacting protein. DEK42 also interacts with the spliceosome component U1-70K. These results suggested that DEK42 participates in the regulation of pre-messenger RNA splicing through its interaction with other spliceosome components. This study showed the function of a newly identified RBP and provided insights into alternative splicing regulation during maize kernel development.

关键词： Dek42 encodes an RNA-binding protein that affects alternative pre-mRNA splicing and maize kernel development^FA Dek42 encodes

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Maize ZmVPP5 is a truncated Vacuole H^＋-PPase that confers hypersensitivity to salt stress

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Journal of Integrative Plant Biology 2016年第6期58卷 518-528页

作者： Xiaoliang Sun Weiwei Qi Yihong Yue Huiling Ling Gang Wang rentao song Shanghai key Laboratory of Bio-Energy Crops School of Life Sciences Shanghai University Shanghai 200444 China Coordinated Crop Biology Research Center(CBRC) Beijing 100193 China

In plants, Vacuole H^＋-PPases（VPPs） are important Aproton pumps and encoded by multiple genes. In addition to full-length VPPs, several truncated forms are expressed, but their biological functions are unknown. In this study, we functionally characterized maize vacuole H^＋-PPase 5（ZmVPP5）, a truncated VPP in the maize genome. Although ZmVPP5 shares high sequence similarity with ZmVPP1 ZmVPP5 lacks the complete structure of the conserved proton transport and the inorganic pyrophosphatase-related domain. Phylogenetic analysis suggests that ZmVPP5 might be derived from an incomplete gene duplication event. ZmVPP5 is expressed in multiple tissues, and ZmVPP5 was detected in the plasma membrane, vacuole membrane and nuclei of maize cells. The overexpression of ZmVPP5 in yeast cells caused a hypersensitivity to salt stress. Transgenic maize lines with overexpressed ZmVPP5 also exhibited the salt hypersensitivity phenotype. A yeast two-hybrid analysis identified the ZmBag6 like protein as a putative ZmVPP5-interacting protein. The results of bimolecular luminescence complementation（Bi LC）assay suggest an interaction between ZmBag6-like protein and ZmVPP5 in vivo. Overall, this study suggests that ZmVPP5 might act as a VPP antagonist and participate in the cellular response to salt stress. Our study of ZmVPP5 has expanded the understanding of the origin and functions of truncated forms of plant VPPs.

关键词： Maize salt stress vacuole H~+-PPases ZmBag6-like protein ZmVPP5

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Dek35 Encodes a PPR Protein that Affects cis-Splicing of Mitochondrial nad4 Intron 1 and Seed Development in Maize

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Molecular Plant 2017年第3期10卷 427-441页

作者： Xinze Chen Fan Feng Weiwei Qi Liming xu Dongsheng Yao Qun Wang rentao song Shanghai Key Laboratory of Bio-Energy Crops School of Life Sciences Shanghai University Shanghai 200444 China National Maize Improvement Center of China China Agricultural University Beijing 100193 China Coordinated Crop Biology Research Center (CBRC) Beijing 100193 China

In higher plants, the splicing of organelle-encoded mRNA involves a complex collaboration with nuclear- encoded proteins. Pentatricopeptide repeat （PPR） proteins have been implicated in these RNA-protein interactions. In this study, we performed the cloning and functional characterization of maize Defective kernel 35 （Dek35）. The dek35-ref mutant is a lethal-seed mutant with developmental deficiency. Dek35 was cloned through Mutator tag isolation and further confirmed by four additional independent mutant alleles. Dek35 encodes an P-type PPR protein that targets the mitochondria. The dek35 mutation causes significant reduction in the accumulation of DEK35 proteins and reduced splicing efficiency of mitochon- drial nad4 intron 1. Analysis of mitochondrial complex in dek35 immature seeds indicated severe deficiency in the complex I assembly and NADH dehydrogenase activity. Transcriptome analysis of dek35 endosperm revealed enhanced expression of genes involved in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function and activity. Collectively, these results indicate that Dek35 encodes an PPR protein that affects the cis-splicing of mitochondrial nad4 intron 1 and is required for mitochondrial function and seed development.

关键词： PPR splicing mitochondria NADH maize

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Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

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Journal of Integrative Plant Biology 2024年第4期66卷 645-659页

作者： Lei Liang Yuancong Wang Yanbin Han Yicong Chen Mengfei Li Yibo Wu Zeyang Ma Han Zhao rentao song State Key Laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100091China Institute of Crop Germplasm and Biotechnology Jiangsu Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing 210014China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China

ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu *** developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental *** MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 *** also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation *** the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter *** Mu-starter genome also improved the assignment of 117,689(54.5%)germinal *** newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal *** insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two *** a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

关键词： ChinaMu Mutator MuT-seq PPR gene Zea mays

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Suppressed 60S ribosome exportation in maize ribosome export associated 1 mutant triggers inconsistent transcriptional and translational regulations

Suppressed 60S ribosome exportation in maize ribosome export...

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第一届全国玉米生物学学术研讨会

作者：祁巍巍 Jie Zhu Qiao Wu rentao song Shanghai Key Laboratory of Bio-Energy Crops School of Life SciencesShanghai University

Ribosome biogenesis is a basal cellular process in eukaryotic *** progress has been made on the biochemistry of ribosome biogenesis,however little is known about the cellular consequences due to impaired ribosome *** ...

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Construction of a BAC library from cucumber (Cucumis sativus L.) and identification of linkage group specific clones

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Progress in Natural Science:Materials International 2008年第2期18卷 143-147页

作者： Yuan Guan a,1,Qi Chen b,1,Junsong Pan a,Zheng Li a,Huanle He a,Aizhong Wu a,rentao song b,Run Cai a,a School of Agriculture and Biology,Shanghai Jiao Tong University,Shanghai 200240,China b School of Life Sciences,Shanghai University,Shanghai 200444,China School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China School of Life Sciences Shanghai University Shanghai 200444 China

A bacterial artificial chromosome (BAC) library consisting of 19,200 clones with an average insert size of 105 kb has been constructed from a cucumber (Cucumis sativus L.) inbred line S94,derived from a cultivar in North China. The entire library was equivalent to approximately 5 haploid cucumber genomes. To facilitate chromosome engineering and anchor the cucumber genetic linkage map to its chromosomes,15 sequence-characterized ampli?ed regions (SCAR) and seven simple sequence repeats (SSR) markers from each link-age group of cucumber were used to screen an ordered array of pooled BAC DNA with polymerase chain reaction (PCR). Fifteen mark-ers gave at least two positive clones. As a result,22 BAC clones representing 7 linkage groups of cucumber were identified,which further validated the genome coverage and utility of the library. This BAC library and linkage group specific clones provide essential resources for future research of the cucumber genome.

关键词： Cucumber BAC library Molecular markers PCR screening Specific clones

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Dek35 encodes a PPR protein that affects cis-splicing of mitochondrial nad4 intron 1 and seed development in maize

Dek35 encodes a PPR protein that affects cis-splicing of mit...

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第十届上海市植物生物学青年学术研讨会

作者： Xinze Chen Fan Feng Weiwei Qi Liming Xu Dongsheng Yao Qun Wang rentao song Shanghai Key Laboratory of Bio-Energy Crops School of Life Sciences Shanghai University National Maize Improvement Center of China China Agricultural University

In higher plants, the splicing of organelle-encoded m RNA involves a complex collaboration with nuclear-encoded proteins. Pentatricopeptide repeat(PPR) proteins have been implicated in these RNA-protein interactions. In this study, we performed cloning and functional characterization of maize Defective kernel 35(Dek35), which encodes a new PPR protein. The dek35-ref mutant is a lethal seed mutant with developmental deficiency. Dek35 was cloned through Mutator tag isolation and was confirmed by four additional independent mutant alleles. Dek35 encodes a new P-type PPR protein that targets mitochondria. The dek35 mutation causes significant reduction of DEK35 proteins, and reduced splicing efficiency of mitochondrial nad4 intron 1. Mitochondrial complex analysis in dek35 immature seeds indicated severe deficiency of complex I assembly and NADH dehydrogenase activity. Transcriptome analysis of dek35 endosperm revealed enhanced expression in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function and activity. The results indicated that Dek35 is a new PPR protein that affects the cis-splicing of mitochondrial nad4 intron 1 and is required for mitochondrial function and seed development.

关键词： PPR splicing mitochondria NADH maize

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Comprehensive proteomic dissection of protein body in maize(Zea mays.) endosperm provides novel insights into its biogenesis

Comprehensive proteomic dissection of protein body in maize(...

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第一届全国玉米生物学学术研讨会

作者：王桂凤 Jiajia Wang Liang Han Fang Wang Nan Xu Hongli Qing Gang Wang rentao song Shanghai Key Laboratory of Bio-Energy Crops School of Life SciencesShanghai University Coordinated Crop Biology Research Center

Seed storage proteins are the main repository for nitrogen and thus provide nutrient source for embryo germination,humans and livestock ***,the major cereal seed storage proteins,accumulate and sequester in ER lumen,and directly form protein bodies(PBs).The content and composition of prolamins are key determinants of grain protein quality and texture related ***,the

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Maize opaque10 encodes a cereal-specific protein essential for the proper distribution of zeins in endosperm protein bodies

Maize opaque10 encodes a cereal-specific protein essential f...

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第十届上海市植物生物学青年学术研讨会

作者： Dongsheng Yao Weiwei Qi Xia Li Qing Yang Shumei Yan Huiling Ling Gang Wang Guifeng Wang rentao song Shanghai Key Laboratory of Bio-Energy Crops School of Life Sciences Shanghai University National Maize Improvement Center of China China Agricultural University

Cereal storage proteins are major nitrogen source for human and livestock. Prolamins are the most abundant storage protein in most cereals. They are deposited into protein boides(PBs) in seed endosperm. So far, the inner structure and the storage mechanism for prolamin PBs remains poorly understood. Maize opaque10(o10) is a classic opaque endosperm mutant with misshapen PBs. Through positional cloning we found O10 encodes a novel cereal-specific PB protein. Its middle domain contains a seven-repeat sequence that is responsible for its dimerization. Its C-terminal of contains a transmembrane motif that is required for its ER localization and PB deposition. A cellular fractionation assay indicated that O10 is initially synthesized in the cytoplasm and then anchored to the ER, and it is eventually deposited in the PB. O10 can interact with 19-k D, 22-k D α-zeins, and 16-k D, 50-k D γ-zeins, through its N-terminal domain. The immunolocalization assay indicated that O10 co-localizes with 16-k D γ-zein and 22-k D α-zein in PB, forming a ring-shaped structure at the interface between the α-zein-rich core and the γ-zein-rich peripheral region. The loss of O10 function disrupts this ring-shaped distribution of 22-k D and 16-k D zeins, resulting in misshapen PBs. These results showed that O10, as a newly evolved PB protein, is essential for the ring-shaped distribution of 22-k D and 16-k D zeins, and controls PB morphology in maize endosperm.

关键词： maize opaque mutant map-based cloning cereal-specific protein PB morphology zein distribution

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