1
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Wang WQ, Liu XF, Zhu YJ, Zhu JZ, Liu C, Wang ZY, Shen XX, Allan AC, Yin XR. Identification of miRNA858 long-loop precursors in seed plants. Plant Cell 2024; 36:1637-1654. [PMID: 38114096 PMCID: PMC11062470 DOI: 10.1093/plcell/koad315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/20/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.
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Affiliation(s)
- Wen-qiu Wang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-fen Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yong-jing Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jia-zhen Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Chao Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zhi-ye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xing-Xing Shen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Xue-ren Yin
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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2
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Wang H, Yu R, Zhu Q, Tian Z, Li F. A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper. Plant J 2024; 118:263-276. [PMID: 38078656 DOI: 10.1111/tpj.16585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 04/02/2024]
Abstract
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as 32P-labeled probe in dot blot and small RNA northern blot experiments. Addition of locked nucleic acids in T4BC33 probe further enhanced its sensitivity in detecting low-abundance miRNAs. With newly developed northern blot method, expression of miR6027 and miR6149 family members was validated. Northern blot analysis also confirmed the successful application of virus-based miRNA silencing in pepper, knocking down accumulation of Can-miR6027a and Can-miR6149L. Importantly, further analysis showed that knocking-down Can-miR6027a led to upregulation of a nucleotide binding-leucine rich repeat domain protein coding gene (CaRLb1) and increased immunity against Phytophthora capsici in pepper leaves. Our study provided a highly sensitive and convenient method for sRNA research and identified new targets for genetic improvement of pepper immunity against P. capsici.
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Affiliation(s)
- Hongzheng Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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3
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Shang B, Li C, Zhang X. How intrinsically disordered proteins order plant gene silencing. Trends Genet 2024; 40:260-275. [PMID: 38296708 PMCID: PMC10932933 DOI: 10.1016/j.tig.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) possess low sequence complexity of amino acids and display non-globular tertiary structures. They can act as scaffolds, form regulatory hubs, or trigger biomolecular condensation to control diverse aspects of biology. Emerging evidence has recently implicated critical roles of IDPs and IDR-contained proteins in nuclear transcription and cytoplasmic post-transcriptional processes, among other molecular functions. We here summarize the concepts and organizing principles of IDPs. We then illustrate recent progress in understanding the roles of key IDPs in machineries that regulate transcriptional and post-transcriptional gene silencing (PTGS) in plants, aiming at highlighting new modes of action of IDPs in controlling biological processes.
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Affiliation(s)
- Baoshuan Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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4
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Zhang T, Li C, Zhu J, Li Y, Wang Z, Tong CY, Xi Y, Han Y, Koiwa H, Peng X, Zhang X. Structured 3' UTRs destabilize mRNAs in plants. Genome Biol 2024; 25:54. [PMID: 38388963 PMCID: PMC10885604 DOI: 10.1186/s13059-024-03186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3' untranslated regions (3' UTRs) of mRNA also hold the key for many aspects of gene regulation. However, there are often contradictory results regarding the roles of RSS in 3' UTRs in gene expression in different organisms and/or contexts. RESULTS Here, we incidentally observe that the primary substrate of miR159a (pri-miR159a), when embedded in a 3' UTR, could promote mRNA accumulation. The enhanced expression is attributed to the earlier polyadenylation of the transcript within the hybrid pri-miR159a-3' UTR and, resultantly, a poorly structured 3' UTR. RNA decay assays indicate that poorly structured 3' UTRs could promote mRNA stability, whereas highly structured 3' UTRs destabilize mRNA in vivo. Genome-wide DMS-MaPseq also reveals the prevailing inverse relationship between 3' UTRs' RSS and transcript accumulation in the transcriptomes of Arabidopsis, rice, and even human. Mechanistically, transcripts with highly structured 3' UTRs are preferentially degraded by 3'-5' exoribonuclease SOV and 5'-3' exoribonuclease XRN4, leading to decreased expression in Arabidopsis. Finally, we engineer different structured 3' UTRs to an endogenous FT gene and alter the FT-regulated flowering time in Arabidopsis. CONCLUSIONS We conclude that highly structured 3' UTRs typically cause reduced accumulation of the harbored transcripts in Arabidopsis. This pattern extends to rice and even mammals. Furthermore, our study provides a new strategy of engineering the 3' UTRs' RSS to modify plant traits in agricultural production and mRNA stability in biotechnology.
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Affiliation(s)
- Tianru Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Xi
- Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA
| | - Yi Han
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Xu Peng
- Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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5
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Chen L, Liu Y, Li S, Ji Y, Sun F, Zou B. DICER-LIKE2 Plays a Crucial Role in Rice Stripe Virus Coat Protein-Mediated Virus Resistance in Arabidopsis. Viruses 2023; 15:2239. [PMID: 38005916 PMCID: PMC10675384 DOI: 10.3390/v15112239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Virus coat protein (CP)-mediated resistance is considered an effective antiviral defense strategy that has been used to develop robust resistance to viral infection. Rice stripe virus (RSV) causes significant losses in rice production in eastern Asia. We previously showed that the overexpression of RSV CP in Arabidopsis plants results in immunity to RSV infection, using the RSV-Arabidopsis pathosystem, and this CP-mediated viral resistance depends on the function of DCLs and is mostly involved in RNA silencing. However, the special role of DCLs in producing t-siRNAs in CP transgenic Arabidopsis plants is not fully understood. In this study, we show that RSV CP transgenic Arabidopsis plants with the dcl2 mutant background exhibited similar virus susceptibility to non-transgenic plants and were accompanied by the absence of transgene-derived small interfering RNAs (t-siRNAs) from the CP region. The dcl2 mutation eliminated the accumulation of CP-derived t-siRNAs, including those generated by other DCL enzymes. In contrast, we also developed RSV CP transgenic Arabidopsis plants with the dcl4 mutant background, and these CP transgenic plants showed immunity to virus infection and accumulated comparable amounts of CP-derived t-siRNAs to CP transgenic Arabidopsis plants with the wild-type background except for a significant increase in the abundance of 22 nt t-siRNA reads. Overall, our data indicate that DCL2 plays an essential, as opposed to redundant, role in CP-derived t-siRNA production and induces virus resistance in RSV CP transgenic Arabidopsis plants.
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Affiliation(s)
- Li Chen
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (S.L.); (Y.J.)
| | - Yanan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (S.L.); (Y.J.)
| | - Shuo Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (S.L.); (Y.J.)
| | - Yinghua Ji
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (S.L.); (Y.J.)
| | - Feng Sun
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (S.L.); (Y.J.)
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
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6
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Chorostecki U, Bologna NG, Ariel F. The plant noncoding transcriptome: a versatile environmental sensor. EMBO J 2023; 42:e114400. [PMID: 37735935 PMCID: PMC10577639 DOI: 10.15252/embj.2023114400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaBarcelonaSpain
| | - Nicolas G. Bologna
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBBarcelonaSpain
| | - Federico Ariel
- Instituto de Agrobiotecnologia del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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7
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Xu C, Zhang Z, He J, Bai Y, Cui J, Liu L, Tang J, Tang G, Chen X, Mo B. The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis. Plant J 2023; 116:144-160. [PMID: 37415266 DOI: 10.1111/tpj.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
RCF1 is a highly conserved DEAD-box RNA helicase found in yeast, plants, and mammals. Studies about the functions of RCF1 in plants are limited. Here, we uncovered the functions of RCF1 in Arabidopsis thaliana as a player in pri-miRNA processing and splicing, as well as in pre-mRNA splicing. A mutant with miRNA biogenesis defects was isolated, and the defect was traced to a recessive point mutation in RCF1 (rcf1-4). We show that RCF1 promotes D-body formation and facilitates the interaction between pri-miRNAs and HYL1. Finally, we show that intron-containing pri-miRNAs and pre-mRNAs exhibit a global splicing defect in rcf1-4. Together, this work uncovers roles for RCF1 in miRNA biogenesis and RNA splicing in Arabidopsis.
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Affiliation(s)
- Chi Xu
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guiliang Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biological Sciences and Biotechnology Research Center, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Xuemei Chen
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
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8
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Zhao G, Niu J, Hai Z, Li T, Xie D, Li Y, Qi Y. Peptidyl-prolyl isomerase Cyclophilin71 promotes SERRATE phase separation and miRNA processing in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2305244120. [PMID: 37639607 PMCID: PMC10483624 DOI: 10.1073/pnas.2305244120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts by the Dicing complex that contains Dicer-like 1 (DCL1), SERRATE (SE), and Hyponastic Leaves 1 (HYL1). The Dicing complex can form nuclear dicing bodies (D-bodies) through SE phase separation. Here, we report that Cyclophilin71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of the Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of peptidyl-prolyl cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.
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Affiliation(s)
- Gaozhan Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Jinrong Niu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Zhuoyan Hai
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Tengfei Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Dongqi Xie
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing100084, China
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9
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Bielewicz D, Dolata J, Bajczyk M, Szewc L, Gulanicz T, Bhat SS, Karlik A, Jozwiak M, Jarmolowski A, Szweykowska-Kulinska Z. Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes. Plant Cell Physiol 2023; 64:571-582. [PMID: 37040378 DOI: 10.1093/pcp/pcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 06/16/2023]
Abstract
Hyponastic Leaves 1 (HYL1) [also known as Double-stranded RNA-Binding protein 1 (DRB1)] is a double-stranded RNA-binding protein involved in microRNA (miRNA) processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the Dicer-Like 1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of miRNA (MIR) genes. HYL1 colocalizes with RNA polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.
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Affiliation(s)
- Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Advanced Technologies, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
| | - Susheel S Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Anna Karlik
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
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10
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Tripathi AM, Singh R, Verma AK, Singh A, Mishra P, Dwivedi V, Narayan S, Gandhivel VHS, Shirke PA, Shivaprasad PV, Roy S. Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing. Plant J 2023; 114:855-874. [PMID: 36883862 DOI: 10.1111/tpj.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 05/27/2023]
Abstract
Small RNAs (sRNAs) such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Several 22-nucleotide miRNAs trigger biogenesis cascades of trans-acting secondary siRNAs, which are involved in various developmental and stress responses. Here we show that Himalayan Arabidopsis thaliana accessions having natural mutations in the miR158 locus exhibit robust cascade silencing of the pentatricopeptide repeat (PPR)-like locus. Furthermore, we show that these cascade sRNAs trigger tertiary silencing of a gene involved in transpiration and stomatal opening. The natural deletions or insertions in MIR158 led to improper processing of miR158 precursors, thereby blocking synthesis of mature miR158. Reduced miR158 levels led to increased levels of its target, a pseudo-PPR gene that is targeted by tasiRNAs generated by the miR173 cascade in other accessions. Using sRNA datasets derived from Indian Himalayan accessions, as well as overexpression and knockout lines of miR158, we show that absence of miR158 led to buildup of pseudo-PPR-derived tertiary sRNAs. These tertiary sRNAs mediated robust silencing of a gene involved in stomatal closure in Himalayan accessions lacking miR158 expression. We functionally validated the tertiary phasiRNA that targets NHX2, which encodes a Na+ -K+ /H+ antiporter protein, thereby regulating transpiration and stomatal conductance. Overall, we report the role of the miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2 pathway in plant adaptation.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajneesh Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Kumar Verma
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akanksha Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Parneeta Mishra
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Varun Dwivedi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Shiv Narayan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Vivek Hari Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Pramod Arvind Shirke
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Sribash Roy
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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11
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Shang B, Wang L, Yan X, Li Y, Li C, Wu C, Wang T, Guo X, Choi SW, Zhang T, Wang Z, Tong CY, Oh T, Zhang X, Wang Z, Peng X, Zhang X. Intrinsically disordered proteins SAID1/2 condensate on SERRATE for dual inhibition of miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2216006120. [PMID: 36972460 PMCID: PMC10083546 DOI: 10.1073/pnas.2216006120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) SAID1/2 are hypothetic dentin sialophosphoprotein-like proteins, but their true functions are unknown. Here, we identified SAID1/2 as negative regulators of SERRATE (SE), a core factor in miRNA biogenesis complex (microprocessor). Loss-of-function double mutants of said1; said2 caused pleiotropic developmental defects and thousands of differentially expressed genes that partially overlapped with those in se. said1; said2 also displayed increased assembly of microprocessor and elevated accumulation of microRNAs (miRNAs). Mechanistically, SAID1/2 promote pre-mRNA processing 4 kinase A-mediated phosphorylation of SE, causing its degradation in vivo. Unexpectedly, SAID1/2 have strong binding affinity to hairpin-structured pri-miRNAs and can sequester them from SE. Moreover, SAID1/2 directly inhibit pri-miRNA processing by microprocessor in vitro. Whereas SAID1/2 did not impact SE subcellular compartmentation, the proteins themselves exhibited liquid-liquid phase condensation that is nucleated on SE. Thus, we propose that SAID1/2 reduce miRNA production through hijacking pri-miRNAs to prevent microprocessor activity while promoting SE phosphorylation and its destabilization in Arabidopsis.
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Affiliation(s)
- Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, College of Life Sciences, Ningbo University, Ningbo315211, China
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Chaohua Wu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Tian Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- College of Life Science, Shandong Normal University, Jinan, Shandong250014, China
| | - Xiang Guo
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng475004, China
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Tianru Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Ziying Wang
- Department of Biology, Texas A&M University, College Station, TX77843
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Taerin Oh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Xiao Zhang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng475004, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Xu Peng
- Department of Medical Physiology, School of Medicine, Texas A&M University, Bryan, TX77807
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- Department of Biology, Texas A&M University, College Station, TX77843
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12
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Xu Y, Chen X. microRNA biogenesis and stabilization in plants. Fundamental Research 2023. [DOI: 10.1016/j.fmre.2023.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
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13
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Nguyen TL, Nguyen TD, Ngo MK, Nguyen TA. Dissection of the Caenorhabditis elegans Microprocessor. Nucleic Acids Res 2023; 51:1512-1527. [PMID: 36598924 PMCID: PMC9976908 DOI: 10.1093/nar/gkac1170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 01/05/2023] Open
Abstract
Microprocessor (MP) is a complex involved in initiating the biogenesis of microRNAs (miRNAs) by cleaving primary microRNAs (pri-miRNAs). miRNAs are small single-stranded RNAs that play a key role in the post-transcriptional regulation of gene expression. Thus, understanding the molecular mechanism of MP is critical for interpreting the roles of miRNAs in normal cellular processes and during the onset of various diseases. MP comprises a ribonuclease enzyme, DROSHA, and a dimeric RNA-binding protein, which is called DGCR8 in humans and Pasha in Caenorhabditis elegans. DROSHA cleaves stem-loop structures located within pri-miRNAs to generate pre-miRNAs. Although the molecular mechanism of human MP (hMP; hDROSHA-DGCR8) is well understood, that of Caenorhabditis elegans MP (cMP; cDrosha-Pasha) is still largely unknown. Here, we reveal the molecular mechanism of cMP and show that it is distinct from that of hMP. We demonstrate that cDrosha and Pasha measure ∼16 and ∼25 bp along a pri-miRNA stem, respectively, and they work together to determine the site of cMP cleavage in pri-miRNAs. We also demonstrate the molecular basis for their substrate measurement. Thus, our findings reveal a previously unknown molecular mechanism of cMP; demonstrate the differences between the mechanisms of hMP and cMP; and provide a foundation for revealing the mechanisms regulating miRNA expression in different animal species.
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Affiliation(s)
- Thuy Linh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Minh Khoa Ngo
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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14
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Jaganathan D, Rajakani R, Doddamani D, Saravanan D, Pulipati S, Hari Sundar G V, Sellamuthu G, Jayabalan S, Kumari K, Parthasarathy P, S P, Ramalingam S, Shivaprasad PV, Venkataraman G. A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance. Sci Rep 2023; 13:2195. [PMID: 36750679 PMCID: PMC9905475 DOI: 10.1038/s41598-023-28836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the 'A10234287911' allele may promote better processing vis-à-vis the structure conferred by 'G10234287911' allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.
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Affiliation(s)
- Deepa Jaganathan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.,Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Raja Rajakani
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | | | - Divya Saravanan
- Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Shalini Pulipati
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Vivek Hari Sundar G
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Gothandapani Sellamuthu
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.,Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Shilpha Jayabalan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Kumkum Kumari
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Pavithra Parthasarathy
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Punitha S
- GIS and Remote Sensing Laboratory, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | | | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.
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15
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Abstract
In plants, microRNAs (miRNAs) associate with ARGONAUTE (AGO) proteins and act as sequence-specific repressors of target gene expression, at the post-transcriptional level through target transcript cleavage and/or translational inhibition. MiRNAs are mainly transcribed by DNA-dependent RNA polymerase II (POL II) and processed by DICER LIKE1 (DCL1) complex into 21∼22 nucleotide (nt) long. Although the main molecular framework of miRNA biogenesis and modes of action have been established, there are still new requirements continually emerging in the recent years. The studies on the involvement factors in miRNA biogenesis indicate that miRNA biogenesis is not accomplished separately step by step, but is closely linked and dynamically regulated with each other. In this article, we will summarize the current knowledge on miRNA biogenesis, including MIR gene transcription, primary miRNA (pri-miRNA) processing, miRNA AGO1 loading and nuclear export; and miRNA metabolism including methylation, uridylation and turnover. We will describe how miRNAs are produced and how the different steps are regulated. We hope to raise awareness that the linkage between different steps and the subcellular regulation are becoming important for the understanding of plant miRNA biogenesis and modes of action.
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16
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Bajczyk M, Jarmolowski A, Jozwiak M, Pacak A, Pietrykowska H, Sierocka I, Swida-Barteczka A, Szewc L, Szweykowska-Kulinska Z. Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation. Plants (Basel) 2023; 12:plants12020342. [PMID: 36679055 PMCID: PMC9864873 DOI: 10.3390/plants12020342] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 05/27/2023]
Abstract
MicroRNAs are small RNAs, 20-22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant's life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evolutionary conservation of miRNA biogenesis core proteins across the plant kingdom.
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17
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Yu Y, Zhang T, Sun J, Jing T, Shen Y, Zhang K, Chen Y, Ding D, Wang G, Yang J, Tang J, Shi Z, Wang D, Gou M. Evolutionary characterization of miR396s in Poaceae exemplified by their genetic effects in wheat and maize. Plant Sci 2022; 325:111465. [PMID: 36155239 DOI: 10.1016/j.plantsci.2022.111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
MiR396s play important roles in regulating plant growth and stress response, and great potential for crop yield promotion was anticipated. For more comprehensive and precise understanding of miR396s in Poaceae, we analyzed the phylogenetic linkage, gene expression, and chromosomal distribution of miR396s in this study. Although the mature miR396s' sequences were mostly conserved, differential expression patterns and chromosomal distribution were found among Poaceae species including the major cereal crops rice, wheat, and maize. Consistently, in comparison with rice, wheat and maize plants transformed with the target mimicry construct of miR396 (MIM396) exhibited differential effects on grain size and disease resistance. While the TaMIM396 plants showed increased grain size, panicle length and sensitivity to B. graminis, the ZmMIM396 plants didn't show obvious changes in grain size and disease resistance. In Addition, several GROWTH-REGULATING FACTOR (GRF) genes in wheat and maize were repressed by miR396s, which could be reversed by MIM396, confirming the conserved regulatory roles of miR396 on GRFs. While providing new solution to enhance grain yield in wheat and revealing potential regulatory variations of miR396s in controlling grain size and disease resistance in different crops, this study gives clues to further explore miR396s' functions in other Poaceae species.
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Affiliation(s)
- Yanwen Yu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Tongxiang Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingfan Sun
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Teng Jing
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanjie Shen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kunpu Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yan Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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18
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Stepien A, Dolata J, Gulanicz T, Bielewicz D, Bajczyk M, Smolinski DJ, Szweykowska-Kulinska Z, Jarmolowski A. Chromatin-associated microprocessor assembly is regulated by the U1 snRNP auxiliary protein PRP40. Plant Cell 2022; 34:4920-4935. [PMID: 36087009 PMCID: PMC9709975 DOI: 10.1093/plcell/koac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
In plants, microRNA (miRNA) biogenesis involves cotranscriptional processing of RNA polymerase II (RNAPII)-generated primary transcripts by a multi-protein complex termed the microprocessor. Here, we report that Arabidopsis (Arabidopsis thaliana) PRE-MRNA PROCESSING PROTEIN 40 (PRP40), the U1 snRNP auxiliary protein, positively regulates the recruitment of SERRATE, a core component of the plant microprocessor, to miRNA genes. The association of DICER-LIKE1 (DCL1), the microprocessor endoribonuclease, with chromatin was altered in prp40ab mutant plants. Impaired cotranscriptional microprocessor assembly was accompanied by RNAPII accumulation at miRNA genes and retention of miRNA precursors at their transcription sites in the prp40ab mutant plants. We show that cotranscriptional microprocessor assembly, regulated by AtPRP40, positively affects RNAPII transcription of miRNA genes and is important to reach the correct levels of produced miRNAs.
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Affiliation(s)
| | | | | | | | - Mateusz Bajczyk
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Dariusz J Smolinski
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun 87-100, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
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Ruiz-Arroyo VM, Nam Y. Dynamic Protein-RNA recognition in primary MicroRNA processing. Curr Opin Struct Biol 2022; 76:102442. [PMID: 36067707 PMCID: PMC9509664 DOI: 10.1016/j.sbi.2022.102442] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
MicroRNAs are prevalent regulators of gene expression, controlling most of the proteome in multicellular organisms. To generate the functional small RNAs, precise processing steps are required. In animals, microRNA biogenesis is initiated by Microprocessor that minimally consists of the Drosha enzyme and its partner, DGCR8. This first step is critical for selecting primary microRNAs, and many RNA-binding proteins and regulatory pathways target both the accuracy and efficiency of microRNA maturation. Structures of Drosha and DGCR8 in complex with primary microRNAs elucidate how RNA structural features rather than sequence provide the framework for substrate recognition. Comparing multiple states of Microprocessor and the closely related Dicer homologs shed light on the dynamic protein-RNA complex assembly and disassembly required to recognize RNAs with diverse sequences via common structural features.
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Affiliation(s)
- Victor M Ruiz-Arroyo
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. https://twitter.com/@Ruiz_Arroy0
| | - Yunsun Nam
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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20
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Akond Z, Rahman H, Ahsan MA, Mosharaf MP, Alam M, Mollah MNH, Borisjuk N. Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.). BioMed Research International 2022; 2022:1-26. [PMID: 36177060 PMCID: PMC9513535 DOI: 10.1155/2022/4955209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.
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21
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Gong Q, Wang Y, Jin Z, Hong Y, Liu Y. Transcriptional and post-transcriptional regulation of RNAi-related gene expression during plant-virus interactions. Stress Biol 2022; 2:33. [PMID: 37676459 PMCID: PMC10441928 DOI: 10.1007/s44154-022-00057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/14/2022] [Indexed: 09/08/2023]
Abstract
As sessile organisms, plants encounter diverse invasions from pathogens including viruses. To survive and thrive, plants have evolved multilayered defense mechanisms to combat virus infection. RNAi, also known as RNA silencing, is an across-kingdom innate immunity and gene regulatory machinery. Molecular framework and crucial roles of RNAi in antiviral defense have been well-characterized. However, it is largely unknown that how RNAi is transcriptionally regulated to initiate, maintain and enhance cellular silencing under normal or stress conditions. Recently, insights into the transcriptional and post-transcriptional regulation of RNAi-related genes in different physiological processes have been emerging. In this review, we integrate these new findings to provide updated views on how plants modulate RNAi machinery at the (post-) transcriptional level to respond to virus infection.
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Affiliation(s)
- Qian Gong
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yunjing Wang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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22
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Ma L, Yang Y, Wang Y, Cheng K, Zhou X, Li J, Zhang J, Li R, Zhang L, Wang K, Zeng N, Gong Y, Zhu D, Deng Z, Qu G, Zhu B, Fu D, Luo Y, Zhu H. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato. Plant Cell 2022; 34:2747-2764. [PMID: 35385118 PMCID: PMC9252502 DOI: 10.1093/plcell/koac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/05/2022] [Indexed: 06/01/2023]
Abstract
Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Yuqiu Wang
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiwen Zhou
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingyu Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Lingling Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ni Zeng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanyan Gong
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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23
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Lukan T, Veillet F, Križnik M, Coll A, Mahkovec Povalej T, Pogačar K, Stare K, Chauvin L, Chauvin JE, Gruden K. CRISPR/Cas9-mediated fine-tuning of miRNA expression in tetraploid potato. Hortic Res 2022; 9:uhac147. [PMID: 36072839 PMCID: PMC9437727 DOI: 10.1093/hr/uhac147] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/27/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs, which modulate the abundance and spatiotemporal accumulation of target mRNAs at transcriptional and post-transcriptional levels and through that play important roles in several biological processes in plants. Here we show that in polyploid species, CRISPR/Cas9 system can be used for fine-tuning of miRNA expression, which can have broader range of applications compared to knock-out mutants. We established the complete pipeline for CRISPR-Cas9-mediated modulation of miRNA expression in potato. It consists of (1) design and assembly of dual sgRNA CRISPR/Cas9 constructs, (2) transient transfection of protoplasts following fast and efficient screening by high resolution melting analysis to select functional sgRNAs, and (3) stable transformation of potato explants with functional sgRNAs and selection of regenerated transgenic lines with desired mutations and desired miRNA abundance based on sequencing and RT-qPCR. We show that miRNA-editing using dual sgRNA approach results in different types of mutations among transgenic lines but also in different alleles of the same plant, which are target site-dependent. The most frequent were short deletions, but we also detected 1-nt insertions (T or G), deletions between two sgRNAs and larger deletions. miRNA abundance correlates with the frequency and type of introduced mutations, as more extensive mutations in more alleles result in lower miRNA abundance. Interestingly, some mutated loci can generate alternative miRNAs, now novel targets were however predicted for those. In all transgenic lines with Cas9 expression, we detected mutations, suggesting high efficiency of Cas9-editing. We confirmed the miRNA-editing efficiency of our optimised approach in two different potato genotypes and three different loci.
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Affiliation(s)
- Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Florian Veillet
- IGEPP, INRAE, Institut Agro, Universite ´ de Rennes, Ploudaniel 29260, France
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Tjaša Mahkovec Povalej
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Karmen Pogačar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Laura Chauvin
- IGEPP, INRAE, Institut Agro, Universite ´ de Rennes, Ploudaniel 29260, France
| | - Jean-Eric Chauvin
- IGEPP, INRAE, Institut Agro, Universite ´ de Rennes, Ploudaniel 29260, France
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
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24
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Zhang BS, Li YC, Guo HS, Zhao JH. Verticillium dahliae Secretes Small RNA to Target Host MIR157d and Retard Plant Floral Transition During Infection. Front Plant Sci 2022; 13:847086. [PMID: 35519822 PMCID: PMC9062233 DOI: 10.3389/fpls.2022.847086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/15/2022] [Indexed: 05/24/2023]
Abstract
Bidirectional trans-kingdom RNA silencing [or RNA interference (RNAi)] plays a key role in plant-pathogen interactions. It has been shown that plant hosts export specific endogenous miRNAs into pathogens to inhibit their virulence, whereas pathogens deliver small RNAs (sRNAs) into plant cells to disturb host immunity. Here, we report a trans-kingdom fungal sRNA retarding host plant floral transition by targeting a miRNA precursor. From Arabidopsis plants infected with Verticillium dahliae, a soil-borne hemibiotrophic pathogenic fungus that causes wilt diseases in a wide range of plant hosts, we obtained a number of possible trans-kingdom V. dahliae sRNAs (VdsRNAs) by sequencing AGO1-immunoprecipitated sRNAs. Among these, a 24-nt VdsRNA derived from V. dahliae rRNA, VdrsR-1, was shown to be an actual trans-kingdom VdsRNA that targets the miR157d precursor MIR157d, resulting in increased rather than reduced miR157d accumulation in V. dahliae-infected plants. Consistent with the miR157 family in the regulation of vegetative and floral transitions by targeting SPL genes in several plant species, we detected two SPL genes, SPL13A/B, that were notably reduced in V. dahliae-infected and VdrsR-1-expressing plants compared with control plants. Furthermore, V. dahliae-infected and VdrsR-1-expressing plants also displayed delayed vegetative phase change and floral transition compared to control plants. Taken together, we disclosed a novel mode of action for a trans-kingdom fungal sRNA, VdrsR-1, which was secreted into host cells to modulate plant floral transition by employing the miR157d/SPL13A/B regulatory module, leading to prolonged host vegetative growth that would undoubtedly benefit fungal propagation.
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Affiliation(s)
- Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Chao Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Hebei University, Baoding, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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25
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Wang Y, Gong Q, Jin Z, Liu Y, Hong Y. Linking calcium and RNAi signaling in plants. Trends Plant Sci 2022; 27:328-330. [PMID: 35078719 DOI: 10.1016/j.tplants.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The genetic link between calcium signaling and RNA interference (RNAi) has remained undiscovered until now. A new study shows that wound-triggered calcium flux acts as an initial messenger for priming RNAi for its role in plant antiviral defense. This paves the way to investigate plant development and response to (a)biotic stresses.
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Affiliation(s)
- Yunjing Wang
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qian Gong
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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26
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Gonzalo L, Tossolini I, Gulanicz T, Cambiagno DA, Kasprowicz-Maluski A, Smolinski DJ, Mammarella MF, Ariel FD, Marquardt S, Szweykowska-Kulinska Z, Jarmolowski A, Manavella PA. R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants. Nat Plants 2022; 8:402-418. [PMID: 35449404 PMCID: PMC9023350 DOI: 10.1038/s41477-022-01125-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/08/2022] [Indexed: 05/03/2023]
Abstract
In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.
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Affiliation(s)
- Lucia Gonzalo
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ileana Tossolini
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Unidad de Estudios Agropecuarios (UDEA), INTA-CONICET, Córdoba, Argentina
| | - Anna Kasprowicz-Maluski
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dariusz Jan Smolinski
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - María Florencia Mammarella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
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27
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Wang L, Yan X, Li Y, Wang Z, Chhajed S, Shang B, Wang Z, Choi SW, Zhao H, Chen S, Zhang X. PRP4KA phosphorylates SERRATE for degradation via 20 S proteasome to fine-tune miRNA production in Arabidopsis. Sci Adv 2022; 8:eabm8435. [PMID: 35333566 PMCID: PMC8956257 DOI: 10.1126/sciadv.abm8435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphorylation can quickly switch on/off protein functions. Here, we reported pre-mRNA processing 4 kinase A (PRP4KA), and its paralogs interact with Serrate (SE), a key factor in RNA processing. PRP4KA phosphorylates at least five residues of SE in vitro and in vivo. Hypophosphorylated, but not hyperphosphorylated, SE variants could readily rescue se phenotypes in vivo. Moreover, hypophosphorylated SE variants had stronger binding affinity to microprocessor component HYL1 and were more resistant to degradation by 20S proteasome than hyperphosphorylated counterparts. Knockdown of the kinases enhanced the accumulation of hypophosphorylated SE. However, the excessive SE interfered with the assembly and function of SE-scaffolded macromolecule complexes, causing the se-like defects in the mutant and wild-type backgrounds. Thus, phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates miRNA metabolism through controlling homeostasis of SE accumulation in plants.
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Affiliation(s)
- Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shweta Chhajed
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hongwei Zhao
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Sixue Chen
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Corresponding author.
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28
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Zhang L, Xiang Y, Chen S, Shi M, Jiang X, He Z, Gao S. Mechanisms of MicroRNA Biogenesis and Stability Control in Plants. Front Plant Sci 2022; 13:844149. [PMID: 35350301 PMCID: PMC8957957 DOI: 10.3389/fpls.2022.844149] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20-24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.
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Affiliation(s)
- Lu Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yu Xiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shengbo Chen
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Min Shi
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xianda Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhuoli He
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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29
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Hirata R, Makabe T, Mishiba KI, Koizumi N, Hamdan SM, Iwata Y. Unpaired nucleotides on the stem of microRNA precursor are important for precise cleavage by Dicer-Like1 in Arabidopsis. Genes Cells 2022; 27:280-292. [PMID: 35143697 DOI: 10.1111/gtc.12927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
Dicer-Like1 (DCL1) is a core component of the plant microRNA (miRNA) biogenesis machinery. MiRNA is transcribed as a precursor RNA, termed primary miRNA (pri-miRNA), which is cleaved by DCL1 in two steps to generate miRNA/miRNA* duplex. Pri-miRNA is a single-stranded RNA that forms a hairpin structure with a number of unpaired bases, hereafter called mismatches, on its stem. In the present study, by using purified recombinant Arabidopsis DCL1, we presented evidence that mismatches on the stem of pri-miRNA are important for precise DCL1 cleavage. We showed that a mismatch at the loop-distal side of the end of miRNA/miRNA* duplex is important for efficient cleavage of pri-miRNA in vitro, as previously suggested in planta. On the other hand, mismatches distant from the miRNA/miRNA* duplex region are important for determining the cleavage position by DCL1. The purified DCL1 proteins cleaved mutant pri-miRNA variants without such mismatches at a position at which wild-type pri-miRNA variants are not usually cleaved, resulting in an increased accumulation of small RNA different from miRNA. Therefore, our results suggest that, in addition to the distance from the ssRNA-dsRNA junction, mismatches on the stem of pri-miRNA function as a determinant for precise processing of pri-miRNA by DCL1 in plants.
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Affiliation(s)
- Rikako Hirata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Tomoya Makabe
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kei-Ichiro Mishiba
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.,Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta-Oecho, Otsu, Shiga, 520-2194, Japan
| | - Nozomu Koizumi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Samir M Hamdan
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yuji Iwata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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30
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Dełeńko K, Nuc P, Kubiak D, Bielewicz D, Dolata J, Niedojadło K, Górka S, Jarmołowski A, Szweykowska-Kulińska Z, Niedojadło J. MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal. BMC Plant Biol 2022; 22:9. [PMID: 34979922 PMCID: PMC8722089 DOI: 10.1186/s12870-021-03323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated. RESULTS In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed. CONCLUSION This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Torun, Poland.
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Dalmadi Á, Miloro F, Bálint J, Várallyay É, Havelda Z. Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis. Nucleic Acids Res 2021; 49:12912-12928. [PMID: 34850097 PMCID: PMC8682782 DOI: 10.1093/nar/gkab1138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/25/2021] [Accepted: 11/16/2021] [Indexed: 11/12/2022] Open
Abstract
Micro RNAs (miRNAs) are processed from precursor RNA molecules with precisely defined secondary stem-loop structures. ARGONAUTE1 (AGO1) is the main executor component of miRNA pathway and its expression is controlled via the auto-regulatory feedback loop activity of miR168 in plants. Previously we have shown that AGO1 loading of miR168 is strongly restricted leading to abundant cytoplasmic accumulation of AGO-unbound miR168. Here, we report, that intrinsic RNA secondary structure of MIR168a precursor not only defines the processing of miR168, but also precisely adjusts AGO1 loading efficiency determining the biologically active subset of miR168 pool. Our results show, that modification of miRNA duplex structure of MIR168a precursor fragment or expression from artificial precursors can alter the finely adjusted loading efficiency of miR168. In dcl1-9 mutant where, except for miR168, production of most miRNAs is severely reduced this mechanism ensures the elimination of unloaded AGO1 proteins via enhanced AGO1 loading of miR168. Based on this data, we propose a new competitive loading mechanism model for miR168 action: the miR168 surplus functions as a molecular buffer for controlled AGO1 loading continuously adjusting the amount of AGO1 protein in accordance with the changing size of the cellular miRNA pool.
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Affiliation(s)
- Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Páter Károly Street 1, Gödöllő 2100, Hungary
| | - Fabio Miloro
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Páter Károly Street 1, Gödöllő 2100, Hungary
| | - Jeannette Bálint
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert Street 4, Gödöllő 2100, Hungary
| | - Éva Várallyay
- Hungarian University of Agriculture and Life Sciences, Institute of Plant Protection, Ménesi Street 44, Budapest 1118, Hungary
| | - Zoltán Havelda
- To whom correspondence should be addressed. Tel: +36 28430494;
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Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y. Structural basis of microRNA processing by Dicer-like 1. Nat Plants 2021; 7:1389-1396. [PMID: 34593993 DOI: 10.1038/s41477-021-01000-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1). With a similar domain architecture as human Dicer, it is mysterious how DCL1 recognizes pri-miRNAs and performs two cleavages sequentially. Here, we report the single-particle cryo-electron microscopy structures of Arabidopsis DCL1 complexed with a pri-miRNA and a pre-miRNA, respectively, in cleavage-competent states. These structures uncover the plasticity of the PAZ domain, which is critical for the recognition of both pri-miRNA and pre-miRNA. These structures suggest that the helicase module serves as an engine that transfers the substrate between two sequential cleavage events. This study lays a foundation for dissecting the regulation mechanism of miRNA biogenesis in plants and provides insights into the dicing state of human Dicer.
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Affiliation(s)
- Xiaobin Wei
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Ke
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Aijia Wen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Gao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Feng
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou, China.
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33
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Xiong F, Groot EP, Zhang Y, Li S. Functions of plant importin β proteins beyond nucleocytoplasmic transport. J Exp Bot 2021; 72:6140-6149. [PMID: 34089597 DOI: 10.1093/jxb/erab263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic cells, nuclear activities are isolated from other cellular functions by the nuclear envelope. Because the nuclear envelope provides a diffusion barrier for macromolecules, a complex nuclear transport machinery has evolved that is highly conserved from yeast to plants and mammals. Among those components, the importin β family is the most important one. In this review, we summarize recent findings on the biological function of importin β family members, including development, reproduction, abiotic stress responses, and plant immunity. In addition to the traditional nuclear transport function, we highlight the new molecular functions of importin β, including protein turnover, miRNA regulation, and signaling. Taken together, our review will provide a systematic view of this versatile protein family in plants.
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Affiliation(s)
- Feng Xiong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Edwin P Groot
- Sino-German Joint Research Center for Agricultural Biology, State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Sha Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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34
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Sun D, Li Y, Ma Z, Yan X, Li N, Shang B, Hu X, Cui K, Koiwa H, Zhang X. The epigenetic factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene silencing in Arabidopsis. Sci Adv 2021; 7:7/32/eabf3898. [PMID: 34348894 PMCID: PMC8336953 DOI: 10.1126/sciadv.abf3898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/15/2021] [Indexed: 05/27/2023]
Abstract
Posttranscriptional gene silencing (PTGS) is a regulatory mechanism to suppress undesired transcripts. Here, we identified Flowering locus VE (FVE), a well-known epigenetic component, as a new player in cytoplasmic PTGS. Loss-of-function fve mutations substantially reduced the accumulation of transgene-derived small interfering RNAs (siRNAs). FVE interacts with suppressor of gene silencing 3 (SGS3), a master component in PTGS. FVE promotes SGS3 homodimerization that is essential for its function. FVE can bind to single-stranded RNA and double-stranded RNA (dsRNA) with moderate affinities, while its truncated form FVE-8 has a significantly increased binding affinity to dsRNA. These affinities affect the association and channeling of SGS3-RNA to downstream dsRNA binding protein 4 (DRB4)/Dicer-like protein 2/4 (DCL2/4) complexes. Hence, FVE, but not FVE-8, biochemically enhances the DRB4/DCL2/4 activity in vitro. We surmise that FVE promotes production of transgene-derived siRNAs through concertedly tuning SGS3-DRB4/DCL2/4 functions. Thus, this study revealed a noncanonical role of FVE in PTGS.
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Affiliation(s)
- Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Niankui Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiaomei Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kai Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, China
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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Owusu Adjei M, Zhou X, Mao M, Rafique F, Ma J. MicroRNAs Roles in Plants Secondary Metabolism. Plant Signal Behav 2021; 16:1915590. [PMID: 33938393 PMCID: PMC8205019 DOI: 10.1080/15592324.2021.1915590] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 05/20/2023]
Abstract
Plant growth and development is dependent on the regulation of classes of microRNAs (miRNAs) that have emerged as important gene regulators. These miRNAs can regulate plant gene expression to function. They play an important roles in biological homeostasis and environmental response controls. A wide range of plant biological and metabolic processes, including developmental timing, tissues specific development, and differentiation, depends on miRNAs. They perpetually regulate secondary metabolite functions in different plant family lines. Mapping of molecular phylogenies shows the distribution of secondary metabolism in the plant territory. More importantly, a lot of information related to miRNA regulatory processes in plants is revealed, but the role of miRNAs in secondary metabolism regulation and functions of the metabolites are still unclear. In this review, we pinnacle some potential miRNAs regulating the secondary metabolite biosynthesis activities in plants. This will provide an alternative knowledge for functional studies of secondary metabolism.
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Affiliation(s)
- Mark Owusu Adjei
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuzixin Zhou
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Meiqin Mao
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fatima Rafique
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Ma
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
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36
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Abstract
The majority of the genome is transcribed to RNA in living organisms. RNA transcripts can form astonishing arrays of secondary and tertiary structures via Watson-Crick, Hoogsteen, or wobble base pairing. In vivo, RNA folding is not a simple thermodynamic event of minimizing free energy. Instead, the process is constrained by transcription, RNA-binding proteins, steric factors, and the microenvironment. RNA secondary structure (RSS) plays myriad roles in numerous biological processes, such as RNA processing, stability, transportation, and translation in prokaryotes and eukaryotes. Emerging evidence has also implicated RSS in RNA trafficking, liquid-liquid phase separation, and plant responses to environmental variations such as temperature and salinity. At molecular level, RSS is correlated with splicing, polyadenylation, protein synthesis, and miRNA biogenesis and functions. In this review, we summarize newly reported methods for probing RSS in vivo and functions and mechanisms of RSS in plant physiology.
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Affiliation(s)
- Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xu Peng
- Department of Medical Physiology, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Correspondence:
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Jodder J. Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant. Plant Cell Rep 2021; 40:783-798. [PMID: 33454802 DOI: 10.1007/s00299-020-02660-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.
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Affiliation(s)
- Jayanti Jodder
- School of Biotechnology, Presidency University (Rajarhat Campus), Canal Bank 7 Road, DG Block, Action Area 1D, Newtown, Kolkata, West Bengal, 700156, India.
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Park SJ, Choi SW, Kim GM, Møller C, Pai HS, Yang SW. Light-stabilized FHA2 suppresses miRNA biogenesis through interactions with DCL1 and HYL1. Mol Plant 2021; 14:647-663. [PMID: 33524550 DOI: 10.1016/j.molp.2021.01.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/21/2020] [Accepted: 01/26/2021] [Indexed: 05/21/2023]
Abstract
The precise regulation of microRNA (miRNA) biogenesis is crucial for plant development, which requires core microprocessors and many fine tuners to coordinate their miRNA processing activity/specificity in fluctuating cellular environments. During de-etiolation, light triggers a dramatic accumulation of core microprocessors and primary miRNAs (pri-miRNAs) but decreases pri-miRNA processing activity, resulting in relatively constant miRNA levels. The mechanisms underlying these seemingly contradictory regulatory changes remain unclear. In this study, we identified forkhead-associated domain 2 (FHA2) as a light-stabilized suppressor of miRNA biogenesis. We found that FHA2 deficiency increased the level of mature miRNAs, accompanied by a reduction in pri-miRNAs and target mRNAs. Biochemical assays showed that FHA2 associates with the core microprocessors DCL1, HYL1, and SE, forming a complex to suppress their pri-miRNA processing activity. Further analyses revealed that FHA2 promotes HYL1 binding but inhibits the binding of DCL1-PAZ-RNase-RNA-binding domains (DCL1-PRR) to miRNAs, whereas FHA2 does not directly bind to these RNAs. Interestingly, we found that FHA2 protein is unstable in the dark but stabilized by light during de-etiolation. Consistently, disruption of FHA led to defects in light-triggered changes in miRNA expression and reduced the survival rate of de-etiolated seedlings after prolonged light deprivation. Collectively, these data suggest that FHA2 is a novel light-stabilized suppressor of miRNA biogenesis and plays a role in fine-tuning miRNA processing during de-etiolation.
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Affiliation(s)
- Seung Jun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Suk Won Choi
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Gu Min Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Christian Møller
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Copenhagen, Denmark; Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
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Abstract
MicroRNAs (miRNAs) are essential non-coding riboregulators of gene expression in plants and animals. In plants, miRNAs guide their effector protein named ARGONAUTE (AGO) to find target RNAs for gene silencing through target RNA cleavage or translational inhibition. miRNAs are derived from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by the DNA-dependent RNA polymerase II. In plants, an RNase III enzyme DICER-LIKE1-containing complex processes pri-miRNAs in the nucleus into miRNAs. To ensure proper function of miRNAs, plants use multiple mechanisms to control miRNA accumulation. On one hand, pri-miRNA levels are controlled through transcription and stability. On the other hand, the activities of the DCL1 complex are regulated by many protein factors at transcriptional, post-transcriptional and post-translational levels. Notably, recent studies reveal that pri-miRNA structure/sequence features and modifications also play important roles in miRNA biogenesis. In this review, we summarize recent progresses on the mechanisms regulating miRNA biogenesis.
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Affiliation(s)
- Mu Li
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska USA
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska USA
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40
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Giudicatti AJ, Tomassi AH, Manavella PA, Arce AL. Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover. Plants (Basel) 2021; 10:plants10020267. [PMID: 33573197 PMCID: PMC7911489 DOI: 10.3390/plants10020267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.
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Deng K, Yin H, Xiong F, Feng L, Dong P, Ren M. Genome-wide miRNA expression profiling in potato ( Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway. PeerJ 2021; 9:e10704. [PMID: 33520467 PMCID: PMC7811781 DOI: 10.7717/peerj.10704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.
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Affiliation(s)
- Kexuan Deng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huan Yin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fangjie Xiong
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Li Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing, China.,Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
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Ciechanowska K, Pokornowska M, Kurzyńska-Kokorniak A. Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases. Int J Mol Sci 2021; 22:E616. [PMID: 33435485 DOI: 10.3390/ijms22020616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.
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Rojas AML, Drusin SI, Chorostecki U, Mateos JL, Moro B, Bologna NG, Bresso EG, Schapire A, Rasia RM, Moreno DM, Palatnik JF. Identification of key sequence features required for microRNA biogenesis in plants. Nat Commun 2020; 11:5320. [PMID: 33087730 PMCID: PMC7577975 DOI: 10.1038/s41467-020-19129-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis. The secondary structure of miRNA precursor sequences is known to affect processing by DICER-like proteins. Here Rojas et al. show that additional sequence features also play a regulatory role in plants with nucleotide identity at unpaired positions substantially impacting processing efficiency.
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Affiliation(s)
- Arantxa M L Rojas
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Salvador I Drusin
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Área Física, Departamento de Química-Física, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Santa Fe, Argentina
| | - Uciel Chorostecki
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, (08034), Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, (08028), Spain
| | - Julieta L Mateos
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, (1428), Argentina
| | - Belén Moro
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, (08193), Spain
| | - Nicolas G Bologna
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, (08193), Spain
| | - Edgardo G Bresso
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Arnaldo Schapire
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Rodolfo M Rasia
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Santa Fe, Argentina
| | - Diego M Moreno
- Instituto de Química de Rosario (CONICET-UNR), Suipacha 570, S2002LRK, Rosario, Santa Fe, Argentina.,Área Química General e Inorgánica, Departamento de Química-Física, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Santa Fe, Argentina
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina. .,Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, 2000, Argentina.
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Wang L, Zhu T, Deal KR, Dvorak J, Luo MC. Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes. Plants (Basel) 2020; 9:E1330. [PMID: 33050178 DOI: 10.3390/plants9101330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.
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Yang Y, Liu X, Wang K, Li J, Zhu G, Ren S, Deng Z, Zhu B, Fu D, Qu G, Luo Y, Zhu H. Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif-containing protein ORRM4 in tomato. New Phytol 2020; 228:570-585. [PMID: 32473605 DOI: 10.1111/nph.16714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Plant organellar RNA editing is a distinct type of post-transcriptional RNA modification that is critical for plant development. We showed previously that the RNA editing factor SlORRM4 is required for mitochondrial function and fruit ripening in tomato (Solanum lycopersicum). However, a comprehensive atlas of the RNA editing mediated by SlORRM4 is lacking. We observed that SlORRM4 is targeted to both chloroplasts and mitochondria, and its knockout results in pale-green leaves and delayed fruit ripening. Using high-throughput sequencing, we identified 12 chloroplast editing sites and 336 mitochondrial editing sites controlled by SlORRM4, accounting for 23% of chloroplast sites in leaves and 61% of mitochondrial sites in fruits, respectively. Analysis of native RNA immunoprecipitation sequencing revealed that SlORRM4 binds to 31 RNA targets; 19 of these targets contain SlORRM4-dependent editing sites. Large-scale analysis of putative SlORRM4-interacting proteins identified SlRIP1b, a RIP/MORF protein. Moreover, functional characterization demonstrated that SlRIP1b is involved in tomato fruit ripening. Our results indicate that SlORRM4 binds to RNA targets and interacts with SlRIP1b to broadly affect RNA editing in tomato organelles. These results provide insights into the molecular and functional diversity of RNA editing factors in higher plants.
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Affiliation(s)
- Yongfang Yang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiuying Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guoning Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Shuang Ren
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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Tomassi AH, Re DA, Romani F, Cambiagno DA, Gonzalo L, Moreno JE, Arce AL, Manavella PA. The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. Plant Physiol 2020; 184:316-329. [PMID: 32636339 PMCID: PMC7479909 DOI: 10.1104/pp.20.00258] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 05/04/2023]
Abstract
In plants, small RNAs are loaded into ARGONAUTE (AGO) proteins to fulfill their regulatory functions. MicroRNAs (miRNAs), one of the most abundant classes of endogenous small RNAs, are preferentially loaded into AGO1. Such loading, long believed to happen exclusively in the cytoplasm, was recently proposed to also occur in the nucleus. Here, we identified CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9), a nuclear-localized, intrinsically disordered protein, as a factor promoting miRNA activity in Arabidopsis (Arabidopsis thaliana). Mutations in the CARP9-encoding gene led to a mild reduction of miRNAs levels, impaired gene silencing, and characteristic morphological defects, including young leaf serration and altered flowering time. Intriguingly, we found that CARP9 was able to interact with HYPONASTIC LEAVES1 (HYL1), but not with other proteins of the miRNA biogenesis machinery. In the same way, CARP9 appeared to interact with mature miRNA, but not with primary miRNA, positioning it after miRNA processing in the miRNA pathway. CARP9 was also able to interact with AGO1, promoting its interaction with HYL1 to facilitate miRNA loading in AGO1. Plants deficient in CARP9 displayed reduced levels of AGO1-loaded miRNAs, partial retention of miRNA in the nucleus, and reduced levels of AGO1. Collectively, our data suggest that CARP9 might modulate HYL1-AGO1 cross talk, acting as a scaffold for the formation of a nuclear post-primary miRNA-processing complex that includes at least HYL1, AGO1, and HEAT SHOCK PROTEIN 90. In such a complex, CARP9 stabilizes AGO1 and mature miRNAs, allowing the proper loading of miRNAs in the effector complex.
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Affiliation(s)
- Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Facundo Romani
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Lucía Gonzalo
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Javier E Moreno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, 3000 Santa Fe, Argentina
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Li Y, Sun D, Ma Z, Yamaguchi K, Wang L, Zhong S, Yan X, Shang B, Nagashima Y, Koiwa H, Han J, Xie Q, Zhou M, Wang Z, Zhang X. Degradation of SERRATE via ubiquitin-independent 20S proteasome to survey RNA metabolism. Nat Plants 2020; 6:970-982. [PMID: 32690892 PMCID: PMC7426255 DOI: 10.1038/s41477-020-0721-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/16/2020] [Indexed: 05/18/2023]
Abstract
SERRATE (SE) is a key factor in RNA metabolism. Here, we report that SE binds 20S core proteasome α subunit G1 (PAG1) among other components and is accumulated in their mutants. Purified PAG1-containing 20S proteasome degrades recombinant SE via an ATP- and ubiquitin-independent manner in vitro. Nevertheless, PAG1 is a positive regulator for SE in vivo, as pag1 shows comparable molecular and/or developmental defects relative to se. Furthermore, SE is poorly assembled into macromolecular complexes, exemplified by the microprocessor in pag1 compared with Col-0. SE overexpression triggered the destruction of both transgenic and endogenous protein, leading to similar phenotypes of se and SE overexpression lines. We therefore propose that PAG1 degrades the intrinsically disordered portion of SE to secure the functionality of folded SE that is assembled and protected in macromolecular complexes. This study provides insight into how the 20S proteasome regulates RNA metabolism through controlling its key factor in eukaryotes.
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Affiliation(s)
- Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Karissa Yamaguchi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Yukihiro Nagashima
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Jiajia Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
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Wang C, Li M, Li G, Liu X, Zhao W, Yu B, Liu J, Yang J, Peng YL. Two distinct nucleic acid binding surfaces of Cdc5 regulate development. Biochem J 2019; 476:3355-68. [PMID: 31652438 DOI: 10.1042/BCJ20190502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 11/17/2022]
Abstract
Cell division cycle 5 (Cdc5) is a highly conserved nucleic acid binding protein among eukaryotes and plays critical roles in development. Cdc5 can simultaneously bind to DNA and RNA by its N-terminal DNA-binding domain (DBD), but molecular mechanisms describing its nucleic acid recognition and the regulation of development through its nucleic acid binding remain unclear. Herein, we present a crystal structure of the N-terminal DBD of MoCdc5 (MoCdc5-DBD) from the rice blast fungus Magnaporthe oryzae. Residue K100 of MoCdc5 is on the periphery of a positively charged groove that is formed by K42, K45, R47, and N92 and is evolutionally conserved. Mutation of K100 significantly reduces the affinity of MoCdc5-DBD to a Cdc5-binding element but not to a conventional myeloblastosis (Myb) domain-binding element, suggesting that K100 is a key residue of the high binding affinity to Cdc5-binding element. Another conserved residue (R31) is located close to the U6 RNA in the structure of the spliceosome, and its mutation dramatically reduces the binding capacity of MoCdc5-DBD for U6 RNA. Importantly, mutations in these key residues, including R31, K42, and K100 in AtCDC5, an Arabidopsis thaliana ortholog of MoCdc5, greatly impair the functions of AtCDC5, resulting in pleiotropic development defects and reduced levels of primary microRNA transcripts. Taken together, our findings suggest that Cdc5-DBD binds nucleic acids with two distinct binding surfaces, one for DNA and another for RNA, which together contribute to establishing the regulation mechanism of Cdc5 on development through nucleic acid binding.
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Narjala A, Nair A, Tirumalai V, Hari Sundar GV, Shivaprasad PV. A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res 2020; 48:3103-3118. [PMID: 32025695 PMCID: PMC7102948 DOI: 10.1093/nar/gkaa077] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.
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Affiliation(s)
- Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
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