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Article ; Online: Programmable RNA N

Shi, Chuanlin / Zou, Wenli / Liu, Xiangpei / Zhang, Hong / Li, Xiaofang / Fu, Guiling / Fei, Qili / Qian, Qian / Shang, Lianguang

Plant biotechnology journal

2024

Abstract: ... ...

Abstract	N
Language	English
Publishing date	2024-02-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7652
ISSN (online)	1467-7652
ISSN	1467-7652
DOI	10.1111/pbi.14307
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: TurboID-mediated proximity labeling for screening interacting proteins of FIP37 in

Li, Xiaofang / Wei, Yanping / Fei, Qili / Fu, Guilin / Gan, Yu / Shi, Chuanlin

Plant direct

2023 Volume 7, Issue 12, Page(s) e555

Abstract: Proximity labeling was recently developed to detect protein-protein interactions and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ... ...

Abstract	Proximity labeling was recently developed to detect protein-protein interactions and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ligase, to a protein of interest (bait protein) to biotinylate adjacent proteins. The biotinylated protein can be purified by streptavidin beads, and identified by mass spectrometry (MS). TurboID is an engineered biotin ligase with high catalytic efficiency, which is used for proximity labeling. Although TurboID-based proximity labeling technology has been successfully established in mammals, its application in plant systems is limited. Here, we report the usage of TurboID for proximity labeling of FIP37, a core member of m
Language	English
Publishing date	2023-12-18
Publishing country	England
Document type	Journal Article
ISSN	2475-4455
ISSN (online)	2475-4455
DOI	10.1002/pld3.555
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae.

Xu, Zhan / Qu, Mingnan / Shi, Chuanlin / Zhang, Hong / Chen, Wu / Qian, Hongge / Zhang, Zhipeng / Qiu, Jiehua / Qian, Qian / Shang, Lianguang

Plant communications

2023 Volume 5, Issue 4, Page(s) 100789

Abstract: Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we ... ...

Abstract	Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we show that rice (Oryza sativa) mesophyll cells are prone to DNA double-stranded breaks (DSBs) in response to ZJ173, a strain of Xanthomonas oryzae pv. oryzae (Xoo). The DSB signal transducer ataxia telangiectasia mutated (ATM), but not the ATM and Rad3-related branch, confers resistance against Xoo. Mechanistically, the MRE11-ATM module phosphorylates suppressor of gamma response 1 (SOG1), which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo infection. Intriguingly, overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining (NHEJ) pathway to the alternative NHEJ and homologous recombination pathways at Xoo-induced DSBs. The enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression lines. Overall, the MRE11-ATM-SOG1 pathway serves as a prime example of plant-pathogen interactions that occur via host non-specific recognition. The function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.
MeSH term(s)	Oryza/metabolism ; Ataxia Telangiectasia ; Phytoalexins ; Signal Transduction ; Xanthomonas
Chemical Substances	Phytoalexins
Language	English
Publishing date	2023-12-29
Publishing country	China
Document type	Journal Article
ISSN	2590-3462
ISSN (online)	2590-3462
DOI	10.1016/j.xplc.2023.100789
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Article ; Online: Temperature‐sensitive male sterility in rice determined by the roles of AGO1d in reproductive phasiRNA biogenesis and function

Shi, Chuanlin / Zhang, Jie / Wu, Bingjin / Jouni, Rachel / Yu, Changxiu / Meyers, Blake C. / Liang, Wanqi / Fei, Qili

New Phytologist. 2022 Nov., v. 236, no. 4 p.1529-1544

2022

Abstract: Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial–temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, ... ...

Abstract	Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial–temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, through histological and high‐throughput sequencing analyses, we show that rice AGO1d, which is specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. AGO1d preferentially binds to miR2118‐triggered 21‐nucleotide (nt) phasiRNAs with a 5′‐terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes a reduction of 21‐ and 24‐nt phasiRNAs and temperature‐sensitive male sterility. At lower temperatures, anthers of the ago1d mutant predominantly show excessive tapetal cells with little starch accumulation during pollen formation, possibly caused by the dysregulation of cell metabolism. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function.
Keywords	biogenesis ; histology ; male sterility ; meiosis ; metabolism ; microRNA ; mutants ; pollen ; rice ; starch ; uridine
Language	English
Dates of publication	2022-11
Size	p. 1529-1544.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18446
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Temperature-sensitive male sterility in rice determined by the roles of AGO1d in reproductive phasiRNA biogenesis and function.

Shi, Chuanlin / Zhang, Jie / Wu, Bingjin / Jouni, Rachel / Yu, Changxiu / Meyers, Blake C / Liang, Wanqi / Fei, Qili

The New phytologist

2022 Volume 236, Issue 4, Page(s) 1529–1544

Abstract: Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial-temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, ... ...

Abstract	Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants, with spatial-temporal specificity. However, the ARGONAUTE (AGO) proteins associated with phasiRNAs and their miRNA triggers remain elusive. Here, through histological and high-throughput sequencing analyses, we show that rice AGO1d, which is specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. AGO1d preferentially binds to miR2118-triggered 21-nucleotide (nt) phasiRNAs with a 5'-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes a reduction of 21- and 24-nt phasiRNAs and temperature-sensitive male sterility. At lower temperatures, anthers of the ago1d mutant predominantly show excessive tapetal cells with little starch accumulation during pollen formation, possibly caused by the dysregulation of cell metabolism. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function.
MeSH term(s)	Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Gene Expression Regulation, Plant ; MicroRNAs/genetics ; Nucleotides/metabolism ; Oryza/genetics ; Oryza/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; RNA, Plant/genetics ; RNA, Small Interfering/metabolism ; Starch/metabolism ; Temperature ; Uridine ; Plant Infertility
Chemical Substances	Argonaute Proteins ; MicroRNAs ; Nucleotides ; Plant Proteins ; RNA, Plant ; RNA, Small Interfering ; Starch (9005-25-8) ; Uridine (WHI7HQ7H85)
Language	English
Publishing date	2022-09-17
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18446
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Synthesis and anticancer activity in vitro and in vivo evaluation of iridium(III) complexes on mouse melanoma B16 cells.

Yuan, Yuhan / Shi, Chuanlin / Wu, Xiaoyun / Li, Wenlong / Huang, Chunxia / Liang, Lijun / Chen, Jing / Wang, Yi / Liu, Yunjun

Journal of inorganic biochemistry

2022 Volume 232, Page(s) 111820

Abstract: Combining the ligand NPIP (2-(2-nitrophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline) with piq (1-phenylisoquinoline) and bzq (benzo[h]quinolone) gave [Ir(piq) ...

Abstract	Combining the ligand NPIP (2-(2-nitrophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline) with piq (1-phenylisoquinoline) and bzq (benzo[h]quinolone) gave [Ir(piq)
MeSH term(s)	Animals ; Antineoplastic Agents/chemistry ; Apoptosis ; Cell Line, Tumor ; Cell Proliferation ; Cisplatin/pharmacology ; Coordination Complexes/chemistry ; Humans ; Iridium/chemistry ; Iridium/pharmacology ; Melanoma ; Mice
Chemical Substances	Antineoplastic Agents ; Coordination Complexes ; Iridium (44448S9773) ; Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2022-04-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2022.111820
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Article: A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway

Shi, Chuan‐Lin / Dong, Nai‐Qian / Guo, Tao / Ye, Wang‐Wei / Shan, Jun‐Xiang / Lin, Hong‐Xuan

plant journal. 2020 Aug., v. 103, no. 3

2020

Abstract: Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several ... ...

Abstract	Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA‐regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT‐box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.
Keywords	Oryza ; biosynthesis ; diterpenoids ; domestication ; grain yield ; growth and development ; panicles ; plant growth ; quantitative trait loci ; quantitative traits ; rice ; spikelets
Language	English
Dates of publication	2020-08
Size	p. 1174-1188.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.14793
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome.

Journal of integrative plant biology

2023 Volume 65, Issue 12, Page(s) 2541–2551

Abstract: Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need ... ...

Abstract	Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hap
MeSH term(s)	Oryza/genetics ; Thermotolerance/genetics ; Phenotype ; Plant Breeding ; Edible Grain/genetics
Language	English
Publishing date	2023-10-25
Publishing country	China (Republic : 1949- )
Document type	Journal Article
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13568
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway.

Shi, Chuan-Lin / Dong, Nai-Qian / Guo, Tao / Ye, Wang-Wei / Shan, Jun-Xiang / Lin, Hong-Xuan

The Plant journal : for cell and molecular biology

2020 Volume 103, Issue 3, Page(s) 1174–1188

Abstract	Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA-regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT-box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.
MeSH term(s)	Cell Enlargement ; Cell Proliferation ; Cloning, Molecular ; Edible Grain/genetics ; Edible Grain/growth & development ; Gene Knockout Techniques ; Genes, Plant/genetics ; Genes, Plant/physiology ; Gibberellins/metabolism ; Oryza/genetics ; Oryza/growth & development ; Oryza/metabolism ; Plant Growth Regulators/metabolism ; Plant Growth Regulators/physiology ; Promoter Regions, Genetic ; Quantitative Trait Loci/genetics ; Quantitative Trait, Heritable
Chemical Substances	Gibberellins ; Plant Growth Regulators
Language	English
Publishing date	2020-05-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.14793
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A centromere map based on super pan-genome highlights the structure and function of rice centromeres.

Lv, Yang / Liu, Congcong / Li, Xiaoxia / Wang, Yueying / He, Huiying / He, Wenchuang / Chen, Wu / Yang, Longbo / Dai, Xiaofan / Cao, Xinglan / Yu, Xiaoman / Liu, Jiajia / Zhang, Bin / Wei, Hua / Zhang, Hong / Qian, Hongge / Shi, Chuanlin / Leng, Yue / Liu, Xiangpei /

Guo, Mingliang / Wang, Xianmeng / Zhang, Zhipeng / Wang, Tianyi / Zhang, Bintao / Xu, Qiang / Cui, Yan / Zhang, Qianqian / Yuan, Qiaoling / Jahan, Noushin / Ma, Jie / Zheng, Xiaoming / Zhou, Yongfeng / Qian, Qian / Guo, Longbiao / Shang, Lianguang

Journal of integrative plant biology

2024 Volume 66, Issue 2, Page(s) 196–207

Abstract: Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a ... ...

Abstract	Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.
MeSH term(s)	DNA, Satellite/metabolism ; Oryza/genetics ; Oryza/metabolism ; Base Sequence ; Centromere/genetics ; Genome, Plant/genetics
Chemical Substances	DNA, Satellite
Language	English
Publishing date	2024-01-29
Publishing country	China (Republic : 1949- )
Document type	Journal Article
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13607
Database	MEDical Literature Analysis and Retrieval System OnLINE

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